T parameter help

[gianfilippo]

Hi,

I am trying to understand the how to properly choose fix the T parameter, which I understand is the min threshold for the O22 value (i.e. observed count of the 2-haplotype).

I am running one SARS-cov-2 sample (amplicon sequencing on Illumina) I am interested in.
I ran it with Tf=0.05 and T=1,10,100. Summary results are below.

Could you please explain me how T is affecting number of SNVs and haplotypes ?

SNVs numbers:
T=100 2412
T=10 3871
T=1 2491

Haplotypes N and freq:
T100:
0_fr_0.2847895994964371, 1_fr_0.19215312905857715, 2_fr_0.19203620837052798, 3_fr_0.1624256254050896, 4_fr_0.06115178494543045, 5_fr_0.05772617687199445
T10:
0_fr_0.2676417679182119, 1_fr_0.26451591468463653, 2_fr_0.15307681215147081, 3_fr_0.08339144250951734, 4_fr_0.08243902008443806, 5_fr_0.08039214779779189, 6_fr_0.06854289485393335
T1:
0_fr_1.0

Thanks

[vtsyvina]

Hello.

The difference in t and tf parameters is that tf is relative to coverage and t is absolute. If a minor haplotype for two positions is supported by less than t reads then it won't be considered in haplotype reconstruction.

With higher parameter T you usually expect the number of haplotypes to decrease(since we consider less "links" between minor positions). However, it depends on the sample and sometimes that one link that appear for lower value of t can actually link two haplotypes that were otherwise(with higher value of t) considered distinct.

I may try to tell you more if you send me logs(to email) while running the tool with "-log" flag. Without them it is difficult to say what exactly is happening in your case.

[gianfilippo]

Hi, thanks for the info. The logfile for the SNV is attached Best Gianfilippo

On Thu, Jan 20, 2022 at 4:21 PM Viachaslau Tsyvina ***@***.***> wrote: Hello. The difference in t and tf parameters is that tf is relative to coverage and t is absolute. If a minor haplotype for two positions is supported by less than t reads then it won't be considered in haplotype reconstruction. With higher parameter T you usually expect the number of haplotypes to decrease(since we consider less "links" between minor positions). However, it depends on the sample and sometimes that one link that appear for lower value of t can actually link two haplotypes that were otherwise(with higher value of t) considered distinct. I may try to tell you more if you send me logs(to email) while running the tool with "-log" flag. Without them it is difficult to say what exactly is happening in your case. — Reply to this email directly, view it on GitHub <#16 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACPSFVH7RJEUZV57NOA75A3UXB4D7ANCNFSM5MLVUZYQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

CliqueSNV version: 2.0.3 Settings: {-m=snv-illumina-vc, -log=true, -in=aln_trimmed_sorted.sam, -outDir=RunT100TF0.05, -t=100, -threads=10, -tf=0.05} Start read sam 0 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 1100000 1200000 1300000 1400000 1500000 1600000 1700000 1800000 1900000 2000000 2100000 DONE Start convert 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 1100000 1200000 1300000 1400000 1500000 1600000 1700000 1800000 1900000 2000000 DONE Total reads number: 2149369 Among them there are 0 paired reads and 2149369 single reads Chimera reads 0 non-chimera paired reads 0 read time 19354 Reference length = 29836 Start 2SNV method Compute profile - DONE 791 Compute SNV data structure - DONE 6077 Common reads matrix calculation 103 200 304 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500 2600 2700 2800 2900 3000 3100 3200 3300 3400 3500 3601 3700 3800 3900 4000 4100 4200 4300 4401 4500 4600 4703 4800 4900 5000 5100 5200 5300 5400 5500 5600 5700 5800 5900 6000 6100 6200 6303 6400 6500 6600 6700 6800 6900 7000 7100 7200 7300 7400 7500 7600 7700 7800 7900 8000 8100 8200 8300 8400 8501 8600 8700 8800 8900 9000 9101 9200 9300 9400 9500 9600 9700 9801 9900 10000 10101 10200 10300 10400 10500 10600 10700 10800 10900 11000 11100 11200 11300 11401 11500 11600 11700 11800 11900 12000 12102 12200 12300 12400 12502 12601 12700 12800 12900 13000 13100 13200 13300 13400 13500 13600 13700 13802 13900 14000 14100 14202 14300 14400 14500 14600 14700 14800 14900 15000 15100 15200 15300 15400 15500 15600 15700 15800 15900 16000 16100 16200 16300 16400 16500 16600 16700 16800 16900 17000 17100 17200 17300 17401 17500 17600 17700 17800 17900 18000 18100 18200 18300 18400 18500 18600 18700 18800 18900 19002 19100 19200 19300 19400 19500 19600 19700 19800 19900 20000 20100 20200 20300 20400 20500 20600 20700 20800 20900 21000 21100 21200 21301 21400 21500 21600 21700 21800 21900 22000 22100 22200 22300 22400 22500 22600 22700 22800 22900 23000 23100 23200 23300 23400 23500 23600 23700 23800 23900 24000 24100 24200 24300 24400 24500 24600 24700 24800 24900 25000 25100 25200 25300 25400 25500 25600 25700 25800 25900 26000 26100 26200 26300 26400 26500 26600 26700 26800 26900 27000 27100 27200 27300 27400 27500 27600 27700 27800 27900 28000 28100 28200 28300 28400 28500 28600 28700 28800 28900 29000 29100 29200 29300 29400 29500 29600 29700 29800 593 597 G T mi1=232 ma1=804 mi2=239 ma2=751 pO=0.000000 r=996 748 5 0 224 false 1.458333 597 631 T C mi1=239 ma1=751 mi2=218 ma2=618 pO=0.000000 r=686 488 20 21 142 false 1.088957 593 631 G C mi1=232 ma1=804 mi2=218 ma2=618 pO=0.000000 r=682 487 23 22 141 false 1.056972 372 385 A A mi1=193 ma1=9.5k mi2=117 ma2=936 pO=0.000000 r=965 721 6 13 103 false 0.646173 3472 3507 A A mi1=395 ma1=12.0k mi2=179 ma2=204 pO=0.000000 r=302 45 24 8 102 false 2.947977 3481 3507 A A mi1=359 ma1=10.6k mi2=179 ma2=204 pO=0.000000 r=350 49 27 21 104 false 2.157676 3492 3507 A A mi1=350 ma1=8.9k mi2=179 ma2=204 pO=0.000000 r=464 143 32 19 115 false 1.657061 3493 3507 T A mi1=198 ma1=8.0k mi2=179 ma2=204 pO=0.000000 r=465 152 25 5 101 false 1.856618 3504 3507 A A mi1=270 ma1=6.6k mi2=179 ma2=204 pO=0.000000 r=494 162 22 29 106 false 1.448087 3500 3507 A A mi1=245 ma1=7.0k mi2=179 ma2=204 pO=0.000000 r=487 160 7 12 112 false 2.372881 3947 4067 G T mi1=2.8k ma1=11.0k mi2=2.9k ma2=10.8k pO=0.000000 r=2651 1816 305 157 354 false 0.483079 6400 6526 A A mi1=837 ma1=51.6k mi2=378 ma2=535 pO=0.000000 r=123 0 1 0 104 false 130.000000 6403 6526 A A mi1=718 ma1=49.6k mi2=378 ma2=535 pO=0.000000 r=128 0 1 0 104 false 130.000000 6406 6526 C A mi1=601 ma1=46.2k mi2=378 ma2=535 pO=0.000000 r=137 1 1 0 108 false 108.000000 6413 6526 G A mi1=673 ma1=47.1k mi2=378 ma2=535 pO=0.000000 r=159 4 4 0 116 false 29.000000 6404 6526 G A mi1=696 ma1=49.7k mi2=378 ma2=535 pO=0.000000 r=132 1 3 0 104 false 40.000000 6412 6526 A A mi1=760 ma1=47.4k mi2=378 ma2=535 pO=0.000000 r=156 3 5 1 118 false 21.851852 6405 6526 T A mi1=685 ma1=49.2k mi2=378 ma2=535 pO=0.000000 r=134 1 1 0 106 false 106.000000 6410 6526 G A mi1=665 ma1=47.6k mi2=378 ma2=535 pO=0.000000 r=153 4 5 0 116 false 24.166667 6409 6526 T A mi1=660 ma1=47.5k mi2=378 ma2=535 pO=0.000000 r=149 3 3 1 112 false 29.473684 6408 6526 C A mi1=640 ma1=47.3k mi2=378 ma2=535 pO=0.000000 r=146 3 2 1 115 false 38.333333 6416 6526 G A mi1=665 ma1=46.0k mi2=378 ma2=535 pO=0.000000 r=173 3 4 0 122 false 32.105263 6418 6526 A A mi1=727 ma1=45.1k mi2=378 ma2=535 pO=0.000000 r=176 3 10 0 126 false 14.651163 6417 6526 T A mi1=665 ma1=45.2k mi2=378 ma2=535 pO=0.000000 r=175 3 11 1 124 false 12.156863 6419 6526 G A mi1=663 ma1=44.9k mi2=378 ma2=535 pO=0.000000 r=179 4 5 0 122 false 25.416667 6422 6526 G A mi1=743 ma1=44.9k mi2=378 ma2=535 pO=0.000000 r=183 5 7 0 125 false 18.939394 6420 6526 T A mi1=662 ma1=45.1k mi2=378 ma2=535 pO=0.000000 r=181 4 5 1 120 false 21.428571 6426 6526 A A mi1=838 ma1=44.1k mi2=378 ma2=535 pO=0.000000 r=200 4 8 1 144 false 18.000000 6427 6526 T A mi1=653 ma1=43.8k mi2=378 ma2=535 pO=0.000000 r=201 4 2 0 133 false 55.416667 6429 6526 C A mi1=682 ma1=43.4k mi2=378 ma2=535 pO=0.000000 r=213 4 11 2 137 false 12.232143 6415 6526 A A mi1=791 ma1=47.3k mi2=378 ma2=535 pO=0.000000 r=164 3 4 0 117 false 30.789474 6430 6526 T A mi1=692 ma1=44.1k mi2=378 ma2=535 pO=0.000000 r=216 4 13 3 136 false 10.000000 6407 6526 T A mi1=638 ma1=47.4k mi2=378 ma2=535 pO=0.000000 r=140 3 3 1 106 false 27.894737 6434 6526 A A mi1=758 ma1=43.4k mi2=378 ma2=535 pO=0.000000 r=232 4 20 5 149 false 7.163462 6435 6526 T A mi1=702 ma1=43.2k mi2=378 ma2=535 pO=0.000000 r=239 6 24 4 144 false 6.101695 6436 6526 A A mi1=775 ma1=42.0k mi2=378 ma2=535 pO=0.000000 r=248 8 13 4 154 false 10.131579 6437 6526 C A mi1=643 ma1=41.6k mi2=378 ma2=535 pO=0.000000 r=252 6 11 1 164 false 15.185185 6438 6526 A A mi1=790 ma1=41.5k mi2=378 ma2=535 pO=0.000000 r=253 4 6 6 167 false 16.057692 6439 6526 G A mi1=690 ma1=40.8k mi2=378 ma2=535 pO=0.000000 r=254 9 22 3 158 false 7.247706 6442 6526 A A mi1=788 ma1=39.8k mi2=378 ma2=535 pO=0.000000 r=263 9 12 4 163 false 11.164384 6444 6526 A A mi1=781 ma1=39.6k mi2=378 ma2=535 pO=0.000000 r=279 7 18 10 165 false 6.932773 6445 6526 C A mi1=638 ma1=39.9k mi2=378 ma2=535 pO=0.000000 r=283 11 11 9 164 false 9.010989 6446 6526 G A mi1=710 ma1=39.7k mi2=378 ma2=535 pO=0.000000 r=293 13 7 1 174 false 19.333333 6448 6526 T A mi1=728 ma1=39.8k mi2=378 ma2=535 pO=0.000000 r=301 11 13 8 166 false 8.736842 6449 6526 C A mi1=664 ma1=39.8k mi2=378 ma2=535 pO=0.000000 r=314 11 15 9 179 false 8.364486 6451 6526 T A mi1=764 ma1=39.8k mi2=378 ma2=535 pO=0.000000 r=320 12 24 2 181 false 7.801724 6452 6526 G A mi1=742 ma1=39.3k mi2=378 ma2=535 pO=0.000000 r=322 11 28 4 187 false 6.726619 6453 6526 A A mi1=831 ma1=39.8k mi2=378 ma2=535 pO=0.000000 r=326 8 9 12 209 false 11.358696 6454 6526 G A mi1=737 ma1=38.6k mi2=378 ma2=535 pO=0.000000 r=342 8 12 12 203 false 9.759615 6455 6526 T A mi1=717 ma1=38.6k mi2=378 ma2=535 pO=0.000000 r=345 6 15 4 208 false 12.682927 6456 6526 G A mi1=727 ma1=38.3k mi2=378 ma2=535 pO=0.000000 r=352 8 19 4 194 false 9.700000 6457 6526 T A mi1=630 ma1=36.9k mi2=378 ma2=535 pO=0.000000 r=354 11 22 8 194 false 7.404580 6459 6526 A A mi1=768 ma1=36.8k mi2=378 ma2=535 pO=0.000000 r=360 18 15 9 215 false 9.429825 6460 6526 T A mi1=645 ma1=37.0k mi2=378 ma2=535 pO=0.000000 r=369 18 28 6 194 false 6.298701 6461 6526 G A mi1=654 ma1=36.3k mi2=378 ma2=535 pO=0.000000 r=372 17 9 0 199 false 18.773585 6462 6526 T A mi1=620 ma1=35.5k mi2=378 ma2=535 pO=0.000000 r=382 15 8 4 214 false 16.984127 6463 6526 G A mi1=655 ma1=35.5k mi2=378 ma2=535 pO=0.000000 r=389 18 28 14 201 false 5.403226 6431 6526 A A mi1=793 ma1=44.0k mi2=378 ma2=535 pO=0.000000 r=219 5 2 1 157 false 46.176471 6467 6526 A A mi1=767 ma1=34.8k mi2=378 ma2=535 pO=0.000000 r=403 16 19 13 219 false 7.604167 6468 6526 C A mi1=574 ma1=33.9k mi2=378 ma2=535 pO=0.000000 r=405 20 30 4 202 false 6.474359 6469 6526 T A mi1=573 ma1=33.4k mi2=378 ma2=535 pO=0.000000 r=417 17 39 3 210 false 5.675676 6470 6526 A A mi1=675 ma1=33.3k mi2=378 ma2=535 pO=0.000000 r=421 11 31 9 206 false 6.023392 6472 6526 C A mi1=600 ma1=33.2k mi2=378 ma2=535 pO=0.000000 r=431 16 24 7 197 false 7.035714 6473 6526 G A mi1=591 ma1=33.3k mi2=378 ma2=535 pO=0.000000 r=434 20 49 3 197 false 4.320175 6475 6526 A A mi1=722 ma1=32.9k mi2=378 ma2=535 pO=0.000000 r=444 20 18 16 219 false 7.019231 6476 6526 G A mi1=583 ma1=32.1k mi2=378 ma2=535 pO=0.000000 r=448 12 30 10 193 false 5.610465 6478 6526 T A mi1=618 ma1=31.9k mi2=378 ma2=535 pO=0.000000 r=461 15 29 5 205 false 6.788079 6479 6526 G A mi1=579 ma1=31.8k mi2=378 ma2=535 pO=0.000000 r=467 20 24 5 205 false 7.536765 6433 6526 C A mi1=703 ma1=44.3k mi2=378 ma2=535 pO=0.000000 r=225 4 19 0 146 false 9.125000 6481 6526 A A mi1=691 ma1=31.8k mi2=378 ma2=535 pO=0.000000 r=479 13 52 25 219 false 3.411215 6480 6526 T A mi1=597 ma1=31.9k mi2=378 ma2=535 pO=0.000000 r=471 22 48 10 205 false 4.035433 6484 6526 A A mi1=659 ma1=30.1k mi2=378 ma2=535 pO=0.000000 r=493 26 34 21 224 false 4.552846 6483 6526 G A mi1=605 ma1=30.8k mi2=378 ma2=535 pO=0.000000 r=488 38 45 1 208 false 4.684685 6485 6526 G A mi1=548 ma1=29.6k mi2=378 ma2=535 pO=0.000000 r=500 24 39 10 207 false 4.704545 6486 6526 A A mi1=644 ma1=29.5k mi2=378 ma2=535 pO=0.000000 r=506 14 13 26 233 false 6.852941 6487 6526 C A mi1=500 ma1=28.5k mi2=378 ma2=535 pO=0.000000 r=516 30 40 6 214 false 5.000000 6488 6526 A A mi1=625 ma1=28.2k mi2=378 ma2=535 pO=0.000000 r=522 19 39 26 227 false 4.068100 6491 6526 A A mi1=650 ma1=27.3k mi2=378 ma2=535 pO=0.000000 r=543 22 27 17 240 false 6.060606 6490 6526 T A mi1=609 ma1=27.6k mi2=378 ma2=535 pO=0.000000 r=534 29 25 15 227 false 6.005291 6493 6526 A A mi1=619 ma1=26.5k mi2=378 ma2=535 pO=0.000000 r=558 20 20 5 247 false 10.291667 6492 6526 T A mi1=540 ma1=27.1k mi2=378 ma2=535 pO=0.000000 r=550 16 50 30 215 false 3.199405 6494 6526 C A mi1=415 ma1=23.2k mi2=378 ma2=535 pO=0.000000 r=566 23 28 8 201 false 6.017964 6496 6526 T A mi1=442 ma1=24.2k mi2=378 ma2=535 pO=0.000000 r=937 379 45 9 209 false 1.756303 6499 6526 A A mi1=505 ma1=23.1k mi2=378 ma2=535 pO=0.000000 r=968 371 26 25 247 false 2.147826 6501 6526 C A mi1=357 ma1=20.8k mi2=378 ma2=535 pO=0.000000 r=988 400 79 13 217 false 1.412760 6502 6526 A A mi1=457 ma1=20.6k mi2=378 ma2=535 pO=0.000000 r=995 394 27 20 267 false 2.293814 6503 6526 G A mi1=325 ma1=20.6k mi2=378 ma2=535 pO=0.000000 r=1003 370 37 6 225 false 2.075646 6504 6526 C A mi1=348 ma1=20.7k mi2=378 ma2=535 pO=0.000000 r=1014 394 79 14 209 false 1.364230 6507 6526 A A mi1=492 ma1=20.5k mi2=378 ma2=535 pO=0.000000 r=1042 403 63 49 250 false 1.468860 6508 6526 T A mi1=343 ma1=20.2k mi2=378 ma2=535 pO=0.000000 r=1045 426 86 4 220 false 1.399491 6511 6526 T A mi1=344 ma1=19.8k mi2=378 ma2=535 pO=0.000000 r=1059 408 67 12 232 false 1.602210 6515 6526 - A mi1=178 ma1=18.5k mi2=378 ma2=535 pO=0.000000 r=1087 419 87 1 149 false 0.966278 6516 6526 T A mi1=343 ma1=18.5k mi2=378 ma2=535 pO=0.000000 r=1091 463 73 16 236 false 1.440781 6521 6526 A A mi1=386 ma1=17.6k mi2=378 ma2=535 pO=0.000000 r=1112 460 38 28 245 false 1.691989 6523 6526 T A mi1=337 ma1=17.1k mi2=378 ma2=535 pO=0.000000 r=1112 453 80 29 232 false 1.304837 6524 6526 A A mi1=374 ma1=16.9k mi2=378 ma2=535 pO=0.000000 r=1114 441 13 35 261 false 2.061611 6443 6526 G A mi1=697 ma1=40.2k mi2=378 ma2=535 pO=0.000000 r=268 13 15 0 154 false 10.547945 6525 6526 C A mi1=245 ma1=17.0k mi2=378 ma2=535 pO=0.000000 r=1114 478 77 3 203 false 1.271930 6512 6526 A A mi1=428 ma1=4.6k mi2=378 ma2=535 pO=0.000000 r=1064 76 47 30 267 false 3.476563 6510 6526 A A mi1=464 ma1=19.9k mi2=378 ma2=535 pO=0.000000 r=1056 416 46 41 253 false 1.655759 6513 6514 - - mi1=14.1k ma1=4.6k mi2=14.1k ma2=4.5k pO=0.000000 r=19079 4403 0 2 14071 false 15.949898 6512 6513 - - mi1=13.9k ma1=4.6k mi2=14.1k ma2=4.6k pO=0.000000 r=19121 4468 0 3 13919 false 15.534598 6512 6514 - - mi1=13.9k ma1=4.6k mi2=14.1k ma2=4.5k pO=0.000000 r=19072 4390 0 2 13917 false 15.821965 8919 8954 T T mi1=210 ma1=10.8k mi2=195 ma2=774 pO=0.000000 r=502 241 11 6 114 false 1.844660 8932 8954 T T mi1=258 ma1=10.0k mi2=195 ma2=774 pO=0.000000 r=666 318 31 36 114 false 0.972696 8935 8954 T T mi1=216 ma1=9.8k mi2=195 ma2=774 pO=0.000000 r=679 330 33 17 103 false 0.971698 8941 8954 T T mi1=214 ma1=9.4k mi2=195 ma2=774 pO=0.000000 r=823 448 34 29 108 false 0.771429 8943 8954 G T mi1=209 ma1=9.2k mi2=195 ma2=774 pO=0.000000 r=832 430 33 23 113 false 0.863914 8944 8954 T T mi1=202 ma1=9.2k mi2=195 ma2=774 pO=0.000000 r=833 453 33 45 100 false 0.653595 8946 8954 A T mi1=223 ma1=9.1k mi2=195 ma2=774 pO=0.000000 r=892 486 5 50 108 false 0.764873 8949 8954 T T mi1=155 ma1=8.4k mi2=195 ma2=774 pO=0.000000 r=989 585 6 19 103 false 0.751825 8951 8954 T T mi1=197 ma1=8.3k mi2=195 ma2=774 pO=0.000000 r=1097 717 26 4 140 false 0.836320 8936 8954 G T mi1=179 ma1=9.7k mi2=195 ma2=774 pO=0.000000 r=695 341 33 10 101 false 0.984405 9463 9557 G T mi1=323 ma1=22.6k mi2=261 ma2=3.9k pO=0.000000 r=423 302 1 1 102 false 1.645161 9470 9557 A T mi1=330 ma1=21.9k mi2=261 ma2=3.9k pO=0.000000 r=447 315 2 2 106 false 1.601208 9466 9557 T T mi1=386 ma1=22.6k mi2=261 ma2=3.9k pO=0.000000 r=434 302 3 7 108 false 1.578947 9473 9557 G T mi1=308 ma1=21.7k mi2=261 ma2=3.9k pO=0.000000 r=549 405 4 1 103 false 1.211765 9474 9557 C T mi1=310 ma1=21.7k mi2=261 ma2=3.9k pO=0.000000 r=549 407 6 0 103 false 1.194896 9478 9557 T T mi1=399 ma1=21.6k mi2=261 ma2=3.9k pO=0.000000 r=568 422 2 2 117 false 1.335616 9480 9557 G T mi1=333 ma1=21.2k mi2=261 ma2=3.9k pO=0.000000 r=571 425 5 5 115 false 1.236559 9481 9557 T T mi1=367 ma1=21.1k mi2=261 ma2=3.9k pO=0.000000 r=571 420 13 2 108 false 1.125000 9482 9557 G T mi1=327 ma1=20.9k mi2=261 ma2=3.9k pO=0.000000 r=572 421 3 3 104 false 1.168539 9484 9557 A T mi1=353 ma1=20.9k mi2=261 ma2=3.9k pO=0.000000 r=573 426 8 2 113 false 1.212446 9485 9557 T T mi1=378 ma1=20.9k mi2=261 ma2=3.9k pO=0.000000 r=574 421 17 10 105 false 0.992439 9486 9557 A T mi1=314 ma1=20.8k mi2=261 ma2=3.9k pO=0.000000 r=576 420 5 3 102 false 1.128319 9487 9557 C T mi1=283 ma1=20.5k mi2=261 ma2=3.9k pO=0.000000 r=578 421 15 0 104 false 1.081081 9488 9557 A T mi1=336 ma1=20.5k mi2=261 ma2=3.9k pO=0.000000 r=578 425 3 1 105 false 1.190476 9489 9557 G T mi1=323 ma1=20.5k mi2=261 ma2=3.9k pO=0.000000 r=580 424 7 7 104 false 1.083333 9490 9557 T T mi1=357 ma1=20.0k mi2=261 ma2=3.9k pO=0.000000 r=580 420 2 5 106 false 1.183036 9492 9557 A T mi1=308 ma1=19.9k mi2=261 ma2=3.9k pO=0.000000 r=582 428 7 3 107 false 1.143162 9493 9557 T T mi1=364 ma1=19.7k mi2=261 ma2=3.9k pO=0.000000 r=582 421 6 5 111 false 1.193548 9494 9557 G T mi1=333 ma1=19.7k mi2=261 ma2=3.9k pO=0.000000 r=585 427 16 1 106 false 1.070707 9495 9557 T T mi1=353 ma1=19.2k mi2=261 ma2=3.9k pO=0.000000 r=588 428 4 4 105 false 1.141304 9497 9557 G T mi1=300 ma1=17.7k mi2=261 ma2=3.9k pO=0.000000 r=590 428 9 2 105 false 1.112288 9499 9557 T T mi1=374 ma1=17.6k mi2=261 ma2=3.9k pO=0.000000 r=595 426 5 7 121 false 1.276371 9502 9557 C T mi1=293 ma1=20.3k mi2=261 ma2=3.9k pO=0.000000 r=1496 1327 9 3 115 false 0.418182 9505 9557 T T mi1=386 ma1=20.2k mi2=261 ma2=3.9k pO=0.000000 r=1505 1320 9 17 124 false 0.435393 9507 9557 A T mi1=340 ma1=20.3k mi2=261 ma2=3.9k pO=0.000000 r=1585 1393 12 7 122 false 0.415248 9508 9557 T T mi1=366 ma1=20.2k mi2=261 ma2=3.9k pO=0.000000 r=1614 1417 20 13 124 false 0.400258 9509 9557 A T mi1=315 ma1=19.9k mi2=261 ma2=3.9k pO=0.000000 r=1642 1439 5 6 116 false 0.391099 9510 9557 C T mi1=281 ma1=19.4k mi2=261 ma2=3.9k pO=0.000000 r=1653 1443 11 3 113 false 0.376918 9513 9557 T T mi1=399 ma1=19.7k mi2=261 ma2=3.9k pO=0.000000 r=1903 1685 14 15 131 false 0.363687 9514 9557 A T mi1=317 ma1=19.6k mi2=261 ma2=3.9k pO=0.000000 r=1917 1687 12 8 122 false 0.345218 9515 9557 C T mi1=284 ma1=19.6k mi2=261 ma2=3.9k pO=0.000000 r=1926 1695 17 12 119 false 0.328548 9516 9557 T T mi1=359 ma1=19.6k mi2=261 ma2=3.9k pO=0.000000 r=1950 1719 10 8 136 false 0.379676 9517 9557 A T mi1=306 ma1=19.6k mi2=261 ma2=3.9k pO=0.000000 r=1971 1741 31 5 122 false 0.323607 9519 9557 T T mi1=421 ma1=19.5k mi2=261 ma2=3.9k pO=0.000000 r=2171 1910 9 22 149 false 0.366273 9521 9557 C T mi1=284 ma1=19.1k mi2=261 ma2=3.9k pO=0.000000 r=2191 1920 28 6 137 false 0.333171 9523 9557 T T mi1=397 ma1=19.0k mi2=261 ma2=3.9k pO=0.000000 r=2260 1984 13 27 144 false 0.335821 9524 9557 A T mi1=333 ma1=19.1k mi2=261 ma2=3.9k pO=0.000000 r=2273 1986 36 26 132 false 0.295434 9525 9557 T T mi1=376 ma1=19.1k mi2=261 ma2=3.9k pO=0.000000 r=2369 2071 12 30 152 false 0.339437 9526 9557 G T mi1=316 ma1=19.2k mi2=261 ma2=3.9k pO=0.000000 r=2472 2190 31 8 136 false 0.289855 9527 9557 T T mi1=365 ma1=18.6k mi2=261 ma2=3.9k pO=0.000000 r=2567 2260 15 26 152 false 0.313531 9528 9557 C T mi1=270 ma1=18.5k mi2=261 ma2=3.9k pO=0.000000 r=2595 2284 16 10 139 false 0.291039 9529 9557 A T mi1=288 ma1=18.5k mi2=261 ma2=3.9k pO=0.000000 r=2603 2306 25 10 148 false 0.302535 9531 9557 T T mi1=402 ma1=17.8k mi2=261 ma2=3.9k pO=0.000000 r=2738 2402 10 35 168 false 0.325329 9535 9557 T T mi1=358 ma1=17.4k mi2=261 ma2=3.9k pO=0.000000 r=3192 2832 13 11 168 false 0.286885 9537 9557 T T mi1=363 ma1=17.4k mi2=261 ma2=3.9k pO=0.000000 r=3345 2973 29 23 169 false 0.265640 9491 9557 C T mi1=277 ma1=20.0k mi2=261 ma2=3.9k pO=0.000000 r=581 424 5 3 104 false 1.140351 9496 9557 A T mi1=334 ma1=19.2k mi2=261 ma2=3.9k pO=0.000000 r=588 429 3 5 109 false 1.182213 9500 9557 G T mi1=301 ma1=17.3k mi2=261 ma2=3.9k pO=0.000000 r=597 424 7 1 106 false 1.162281 10622 10737 A A mi1=310 ma1=17.0k mi2=285 ma2=950 pO=0.000000 r=125 11 0 2 103 false 27.105263 10630 10737 A A mi1=313 ma1=16.4k mi2=285 ma2=950 pO=0.000000 r=159 28 1 3 113 false 12.840909 10631 10737 G A mi1=304 ma1=16.4k mi2=285 ma2=950 pO=0.000000 r=162 32 2 1 100 false 11.363636 10632 10737 C A mi1=286 ma1=16.0k mi2=285 ma2=950 pO=0.000000 r=163 34 2 0 101 false 12.023810 10633 10737 A A mi1=308 ma1=16.0k mi2=285 ma2=950 pO=0.000000 r=165 36 2 0 102 false 11.590909 10618 10737 G A mi1=300 ma1=16.8k mi2=285 ma2=950 pO=0.000000 r=111 4 1 1 102 false 42.500000 10635 10737 C A mi1=283 ma1=15.9k mi2=285 ma2=950 pO=0.000000 r=171 36 0 3 101 false 10.520833 10634 10737 G A mi1=290 ma1=15.9k mi2=285 ma2=950 pO=0.000000 r=168 36 2 2 101 false 9.711538 10636 10737 T A mi1=318 ma1=16.2k mi2=285 ma2=950 pO=0.000000 r=179 44 2 2 101 false 8.416667 10638 10737 G A mi1=315 ma1=16.2k mi2=285 ma2=950 pO=0.000000 r=197 54 1 0 119 false 10.258621 10639 10737 T A mi1=338 ma1=16.1k mi2=285 ma2=950 pO=0.000000 r=197 50 3 2 103 false 7.357143 10640 10737 A A mi1=300 ma1=15.9k mi2=285 ma2=950 pO=0.000000 r=198 51 5 3 105 false 6.325301 10641 10737 C A mi1=301 ma1=16.1k mi2=285 ma2=950 pO=0.000000 r=206 60 0 0 107 false 8.916667 10643 10737 G A mi1=316 ma1=16.1k mi2=285 ma2=950 pO=0.000000 r=217 63 2 3 118 false 7.108434 10644 10737 A A mi1=322 ma1=16.1k mi2=285 ma2=950 pO=0.000000 r=224 62 0 6 107 false 6.220930 10645 10737 C A mi1=290 ma1=15.8k mi2=285 ma2=950 pO=0.000000 r=224 63 16 4 109 false 3.811189 10646 10737 A A mi1=327 ma1=16.0k mi2=285 ma2=950 pO=0.000000 r=232 71 16 4 109 false 3.609272 10647 10737 C A mi1=279 ma1=16.0k mi2=285 ma2=950 pO=0.000000 r=236 68 14 3 111 false 4.080882 10649 10737 A A mi1=346 ma1=16.5k mi2=285 ma2=950 pO=0.000000 r=255 84 7 2 126 false 5.250000 10650 10737 C A mi1=307 ma1=16.3k mi2=285 ma2=950 pO=0.000000 r=264 84 6 6 118 false 4.469697 10651 10737 T A mi1=320 ma1=16.2k mi2=285 ma2=950 pO=0.000000 r=268 85 1 3 121 false 5.990099 10652 10737 A A mi1=345 ma1=16.1k mi2=285 ma2=950 pO=0.000000 r=273 89 23 4 122 false 3.096447 10654 10737 T A mi1=342 ma1=16.1k mi2=285 ma2=950 pO=0.000000 r=277 85 8 9 140 false 4.575163 10655 10737 A A mi1=329 ma1=16.0k mi2=285 ma2=950 pO=0.000000 r=284 85 4 6 121 false 4.840000 10656 10737 C A mi1=285 ma1=15.6k mi2=285 ma2=950 pO=0.000000 r=287 84 26 5 119 false 2.860577 10657 10737 A A mi1=317 ma1=15.5k mi2=285 ma2=950 pO=0.000000 r=292 91 1 8 125 false 4.921260 10658 10737 G A mi1=299 ma1=14.4k mi2=285 ma2=950 pO=0.000000 r=299 97 4 14 120 false 3.550296 10660 10737 T A mi1=323 ma1=14.3k mi2=285 ma2=950 pO=0.000000 r=315 98 10 9 137 false 3.936782 10662 10737 A A mi1=332 ma1=14.3k mi2=285 ma2=950 pO=0.000000 r=321 102 2 12 145 false 4.588608 10663 10737 T A mi1=304 ma1=14.4k mi2=285 ma2=950 pO=0.000000 r=328 107 5 4 121 false 4.230769 10664 10737 G A mi1=295 ma1=14.3k mi2=285 ma2=950 pO=0.000000 r=332 103 22 5 125 false 2.962085 10668 10737 T A mi1=320 ma1=14.0k mi2=285 ma2=950 pO=0.000000 r=344 121 11 10 143 false 3.487805 10669 10737 A A mi1=320 ma1=14.0k mi2=285 ma2=950 pO=0.000000 r=349 104 4 18 130 false 3.385417 10670 10737 G A mi1=293 ma1=13.9k mi2=285 ma2=950 pO=0.000000 r=353 111 6 10 125 false 3.571429 10671 10737 C A mi1=286 ma1=13.8k mi2=285 ma2=950 pO=0.000000 r=356 112 7 10 127 false 3.527778 10673 10737 T A mi1=323 ma1=13.5k mi2=285 ma2=950 pO=0.000000 r=358 113 4 8 150 false 4.658385 10675 10737 G A mi1=308 ma1=13.5k mi2=285 ma2=950 pO=0.000000 r=361 108 11 10 141 false 3.671875 10677 10737 T A mi1=324 ma1=13.4k mi2=285 ma2=950 pO=0.000000 r=374 108 16 19 147 false 2.963710 10679 10737 T A mi1=315 ma1=13.3k mi2=285 ma2=950 pO=0.000000 r=382 109 9 14 134 false 3.333333 10680 10737 A A mi1=305 ma1=13.2k mi2=285 ma2=950 pO=0.000000 r=384 117 7 15 126 false 3.073171 10681 10737 C A mi1=274 ma1=13.0k mi2=285 ma2=950 pO=0.000000 r=388 112 12 6 132 false 3.586957 10682 10737 G A mi1=284 ma1=12.9k mi2=285 ma2=950 pO=0.000000 r=391 117 17 13 124 false 2.616034 10684 10737 T A mi1=291 ma1=11.5k mi2=285 ma2=950 pO=0.000000 r=399 126 10 18 134 false 2.815126 10683 10737 C A mi1=256 ma1=11.5k mi2=285 ma2=950 pO=0.000000 r=394 119 9 11 131 false 3.291457 10685 10737 G A mi1=258 ma1=11.4k mi2=285 ma2=950 pO=0.000000 r=405 111 4 19 135 false 3.325123 10686 10737 C A mi1=248 ma1=11.3k mi2=285 ma2=950 pO=0.000000 r=411 118 10 21 125 false 2.582645 10687 10737 T A mi1=262 ma1=11.3k mi2=285 ma2=950 pO=0.000000 r=416 119 4 10 141 false 4.028571 10688 10737 G A mi1=262 ma1=13.1k mi2=285 ma2=950 pO=0.000000 r=808 496 39 16 131 false 0.914804 10690 10737 T A mi1=294 ma1=13.0k mi2=285 ma2=950 pO=0.000000 r=826 522 22 8 152 false 1.183801 10691 10737 A A mi1=285 ma1=12.8k mi2=285 ma2=950 pO=0.000000 r=830 510 32 25 142 false 0.962060 10692 10737 T A mi1=274 ma1=12.7k mi2=285 ma2=950 pO=0.000000 r=836 524 39 20 131 false 0.861842 10695 10737 A A mi1=342 ma1=12.5k mi2=285 ma2=950 pO=0.000000 r=874 543 14 17 169 false 1.266867 10696 10737 T A mi1=255 ma1=11.7k mi2=285 ma2=950 pO=0.000000 r=894 552 5 12 143 false 1.153226 10698 10737 G A mi1=258 ma1=11.5k mi2=285 ma2=950 pO=0.000000 r=914 572 27 9 157 false 1.096369 10699 10737 A A mi1=261 ma1=11.6k mi2=285 ma2=950 pO=0.000000 r=935 584 33 21 140 false 0.875000 10700 10737 G A mi1=244 ma1=11.6k mi2=285 ma2=950 pO=0.000000 r=941 590 33 9 147 false 0.969657 10701 10737 A A mi1=270 ma1=11.5k mi2=285 ma2=950 pO=0.000000 r=967 587 14 22 146 false 0.998632 10702 10737 C A mi1=223 ma1=11.4k mi2=285 ma2=950 pO=0.000000 r=974 607 35 16 140 false 0.863132 10705 10737 G A mi1=269 ma1=11.3k mi2=285 ma2=950 pO=0.000000 r=1047 642 24 23 164 false 0.987952 10706 10737 T A mi1=290 ma1=11.2k mi2=285 ma2=950 pO=0.000000 r=1054 648 51 28 152 false 0.788382 10708 10737 G A mi1=277 ma1=11.0k mi2=285 ma2=950 pO=0.000000 r=1069 669 21 26 162 false 0.945158 10711 10737 T A mi1=306 ma1=10.8k mi2=285 ma2=950 pO=0.000000 r=1095 655 16 25 188 false 1.147741 10712 10737 C A mi1=208 ma1=10.6k mi2=285 ma2=950 pO=0.000000 r=1099 673 46 22 145 false 0.767196 10713 10737 T A mi1=277 ma1=10.5k mi2=285 ma2=950 pO=0.000000 r=1110 658 31 46 163 false 0.843685 10714 10737 C A mi1=204 ma1=10.5k mi2=285 ma2=950 pO=0.000000 r=1117 678 24 6 152 false 0.952381 10716 10737 A A mi1=268 ma1=10.5k mi2=285 ma2=950 pO=0.000000 r=1132 677 27 20 177 false 1.023121 10717 10737 T A mi1=266 ma1=10.3k mi2=285 ma2=950 pO=0.000000 r=1151 680 36 19 150 false 0.833333 10718 10737 C A mi1=215 ma1=10.3k mi2=285 ma2=950 pO=0.000000 r=1162 679 43 17 142 false 0.772579 10719 10737 G A mi1=243 ma1=10.3k mi2=285 ma2=950 pO=0.000000 r=1200 719 12 26 158 false 0.907003 10720 10737 A A mi1=255 ma1=10.3k mi2=285 ma2=950 pO=0.000000 r=1204 734 23 25 162 false 0.874730 10723 10737 T A mi1=294 ma1=10.1k mi2=285 ma2=950 pO=0.000000 r=1236 740 33 29 183 false 0.926113 10678 10737 G A mi1=292 ma1=13.3k mi2=285 ma2=950 pO=0.000000 r=379 116 24 24 132 false 2.142857 10724 10737 A A mi1=244 ma1=10.1k mi2=285 ma2=950 pO=0.000000 r=1265 762 14 7 172 false 1.016548 10726 10737 C A mi1=240 ma1=9.8k mi2=285 ma2=950 pO=0.000000 r=1275 767 39 16 170 false 0.861196 10728 10737 C A mi1=211 ma1=9.0k mi2=285 ma2=950 pO=0.000000 r=1321 810 58 25 155 false 0.678634 10730 10737 A A mi1=271 ma1=9.0k mi2=285 ma2=950 pO=0.000000 r=1368 856 29 18 191 false 0.914751 10731 10737 C A mi1=213 ma1=8.9k mi2=285 ma2=950 pO=0.000000 r=1368 872 20 20 152 false 0.736434 10732 10737 T A mi1=241 ma1=8.9k mi2=285 ma2=950 pO=0.000000 r=1392 863 62 30 156 false 0.633631 10733 10737 C A mi1=196 ma1=8.6k mi2=285 ma2=950 pO=0.000000 r=1392 889 52 26 151 false 0.628643 10735 10737 T A mi1=248 ma1=8.5k mi2=285 ma2=950 pO=0.000000 r=1392 876 49 27 186 false 0.788136 10703 10737 A A mi1=281 ma1=11.4k mi2=285 ma2=950 pO=0.000000 r=990 617 8 24 159 false 1.067114 10727 10737 A A mi1=268 ma1=9.6k mi2=285 ma2=950 pO=0.000000 r=1307 798 45 34 165 false 0.740575 11200 11331 G G mi1=7.3k ma1=25.4k mi2=7.7k ma2=22.8k pO=0.000000 r=4439 2374 1224 279 480 false 0.286191 11275 11372 T G mi1=675 ma1=32.9k mi2=214 ma2=1.4k pO=0.000000 r=189 35 1 7 101 false 7.537313 11278 11372 T G mi1=634 ma1=32.9k mi2=214 ma2=1.4k pO=0.000000 r=198 31 1 7 103 false 8.174603 11282 11372 A G mi1=476 ma1=9.7k mi2=214 ma2=1.4k pO=0.000000 r=205 12 2 4 101 false 14.027778 11286 11287 - - mi1=23.0k ma1=8.0k mi2=23.0k ma2=8.1k pO=0.000000 r=31471 7930 0 4 22967 false 14.451925 11283 11284 - - mi1=22.9k ma1=9.8k mi2=23.0k ma2=9.8k pO=0.000000 r=33004 9490 20 0 22920 false 11.974922 11282 11283 - - mi1=22.6k ma1=9.7k mi2=22.9k ma2=9.8k pO=0.000000 r=33112 9575 5 0 22636 false 11.795727 11285 11286 - - mi1=23.0k ma1=9.4k mi2=23.0k ma2=8.0k pO=0.000000 r=31476 7932 3 0 22967 false 14.455564 11284 11285 - - mi1=23.0k ma1=9.8k mi2=23.0k ma2=9.4k pO=0.000000 r=32634 9239 2 0 22965 false 12.417541 11292 11372 G G mi1=521 ma1=31.8k mi2=214 ma2=1.4k pO=0.000000 r=229 52 5 6 101 false 5.260417 11286 11288 - - mi1=23.0k ma1=8.0k mi2=23.0k ma2=8.0k pO=0.000000 r=31410 7850 0 11 22959 false 14.542057 11282 11284 - - mi1=22.6k ma1=9.7k mi2=23.0k ma2=9.8k pO=0.000000 r=33002 9464 25 0 22636 false 11.833961 11284 11286 - - mi1=23.0k ma1=9.8k mi2=23.0k ma2=8.0k pO=0.000000 r=31472 7936 6 0 22965 false 14.425251 11286 11289 - - mi1=23.0k ma1=8.0k mi2=23.0k ma2=8.1k pO=0.000000 r=31405 7863 0 17 22953 false 14.470432 11282 11285 - - mi1=22.6k ma1=9.7k mi2=23.0k ma2=9.4k pO=0.000000 r=32629 9074 27 0 22636 false 12.326291 11296 11372 T G mi1=682 ma1=31.6k mi2=214 ma2=1.4k pO=0.000000 r=243 48 2 11 104 false 5.200000 11284 11287 - - mi1=23.0k ma1=9.8k mi2=23.0k ma2=8.1k pO=0.000000 r=31447 7976 6 4 22961 false 14.321981 11298 11372 A G mi1=522 ma1=32.2k mi2=214 ma2=1.4k pO=0.000000 r=261 62 3 12 103 false 4.221311 11286 11290 - - mi1=23.0k ma1=8.0k mi2=23.0k ma2=7.9k pO=0.000000 r=31385 7811 1 12 22953 false 14.595574 11282 11286 - - mi1=22.6k ma1=9.7k mi2=23.0k ma2=8.0k pO=0.000000 r=31467 7910 30 0 22636 false 14.094645 11299 11372 G G mi1=517 ma1=32.3k mi2=214 ma2=1.4k pO=0.000000 r=268 59 0 9 108 false 5.684211 11284 11288 - - mi1=23.0k ma1=9.8k mi2=23.0k ma2=8.0k pO=0.000000 r=31386 7850 6 11 22953 false 14.494190 11300 11372 C G mi1=477 ma1=32.3k mi2=214 ma2=1.4k pO=0.000000 r=273 65 3 9 108 false 4.778761 11282 11287 - - mi1=22.6k ma1=9.7k mi2=23.0k ma2=8.1k pO=0.000000 r=31442 7914 30 4 22632 false 14.057143 11284 11289 - - mi1=23.0k ma1=9.8k mi2=23.0k ma2=8.1k pO=0.000000 r=31381 7916 7 17 22947 false 14.320394 11287 11288 - - mi1=23.0k ma1=8.1k mi2=23.0k ma2=8.0k pO=0.000000 r=31414 7861 0 8 22961 false 14.545167 11301 11372 T G mi1=664 ma1=32.1k mi2=214 ma2=1.4k pO=0.000000 r=279 68 3 14 110 false 4.044118 11283 11285 - - mi1=22.9k ma1=9.8k mi2=23.0k ma2=9.4k pO=0.000000 r=32631 9153 22 0 22920 false 12.401255 11285 11287 - - mi1=23.0k ma1=9.4k mi2=23.0k ma2=8.1k pO=0.000000 r=31451 7988 5 4 22963 false 14.308948 11282 11288 - - mi1=22.6k ma1=9.7k mi2=23.0k ma2=8.0k pO=0.000000 r=31381 7819 30 11 22624 false 14.170111 11305 11372 A G mi1=565 ma1=32.4k mi2=214 ma2=1.4k pO=0.000000 r=307 70 4 5 112 false 5.283019 11284 11290 - - mi1=23.0k ma1=9.8k mi2=23.0k ma2=7.9k pO=0.000000 r=31361 7817 8 12 22947 false 14.528935 11287 11289 - - mi1=23.0k ma1=8.1k mi2=23.0k ma2=8.1k pO=0.000000 r=31409 7942 1 14 22955 false 14.343289 11306 11372 G G mi1=530 ma1=32.3k mi2=214 ma2=1.4k pO=0.000000 r=310 69 1 14 114 false 4.418605 11288 11289 - - mi1=23.0k ma1=8.0k mi2=23.0k ma2=8.1k pO=0.000000 r=31444 7931 0 6 22955 false 14.428033 11307 11372 A G mi1=505 ma1=31.8k mi2=214 ma2=1.4k pO=0.000000 r=314 66 0 8 114 false 5.816327 11289 11290 - - mi1=23.0k ma1=8.1k mi2=23.0k ma2=7.9k pO=0.000000 r=31431 7875 1 0 22956 false 14.567839 11282 11289 - - mi1=22.6k ma1=9.7k mi2=23.0k ma2=8.1k pO=0.000000 r=31376 7837 31 17 22618 false 14.085191 11308 11372 C G mi1=485 ma1=31.8k mi2=214 ma2=1.4k pO=0.000000 r=318 89 6 0 115 false 5.088496 11288 11290 - - mi1=23.0k ma1=8.0k mi2=23.0k ma2=7.9k pO=0.000000 r=31424 7813 1 6 22955 false 14.637801 11309 11372 T G mi1=670 ma1=31.6k mi2=214 ma2=1.4k pO=0.000000 r=324 72 1 25 120 false 3.409091 11282 11290 - - mi1=22.6k ma1=9.7k mi2=23.0k ma2=7.9k pO=0.000000 r=31356 7777 32 12 22618 false 14.219791 11310 11372 G G mi1=525 ma1=31.6k mi2=214 ma2=1.4k pO=0.000000 r=328 75 4 13 117 false 4.090909 11311 11372 T G mi1=612 ma1=31.5k mi2=214 ma2=1.4k pO=0.000000 r=331 74 6 21 115 false 3.159341 11312 11372 G G mi1=521 ma1=31.5k mi2=214 ma2=1.4k pO=0.000000 r=334 77 7 20 115 false 3.108108 11314 11372 T G mi1=631 ma1=30.9k mi2=214 ma2=1.4k pO=0.000000 r=343 71 3 17 115 false 3.807947 11315 11372 A G mi1=506 ma1=31.0k mi2=214 ma2=1.4k pO=0.000000 r=346 83 9 10 114 false 3.584906 11316 11372 T G mi1=586 ma1=30.7k mi2=214 ma2=1.4k pO=0.000000 r=351 80 5 15 120 false 3.750000 11317 11372 G G mi1=495 ma1=30.6k mi2=214 ma2=1.4k pO=0.000000 r=355 74 10 15 115 false 3.304598 11319 11372 A G mi1=469 ma1=29.2k mi2=214 ma2=1.4k pO=0.000000 r=368 80 4 10 123 false 4.522059 11318 11372 T G mi1=591 ma1=29.2k mi2=214 ma2=1.4k pO=0.000000 r=363 69 5 20 118 false 3.491124 11320 11372 T G mi1=547 ma1=28.3k mi2=214 ma2=1.4k pO=0.000000 r=374 74 3 16 123 false 4.100000 11321 11372 G G mi1=495 ma1=28.0k mi2=214 ma2=1.4k pO=0.000000 r=380 67 2 4 119 false 6.538462 11322 11372 C G mi1=421 ma1=28.0k mi2=214 ma2=1.4k pO=0.000000 r=388 70 3 2 120 false 6.666667 11323 11372 A G mi1=456 ma1=27.5k mi2=214 ma2=1.4k pO=0.000000 r=394 79 9 16 113 false 3.156425 11324 11372 T G mi1=570 ma1=27.3k mi2=214 ma2=1.4k pO=0.000000 r=395 77 0 30 120 false 3.045685 11325 11372 C G mi1=386 ma1=26.9k mi2=214 ma2=1.4k pO=0.000000 r=399 74 9 7 112 false 4.057971 11326 11372 A G mi1=467 ma1=26.9k mi2=214 ma2=1.4k pO=0.000000 r=410 71 10 12 116 false 3.647799 11327 11372 G G mi1=480 ma1=26.7k mi2=214 ma2=1.4k pO=0.000000 r=415 68 1 13 119 false 4.798387 11328 11372 C G mi1=409 ma1=26.6k mi2=214 ma2=1.4k pO=0.000000 r=421 86 6 11 112 false 3.636364 11329 11372 T G mi1=557 ma1=26.5k mi2=214 ma2=1.4k pO=0.000000 r=428 76 9 30 128 false 2.758621 11330 11372 G G mi1=465 ma1=26.4k mi2=214 ma2=1.4k pO=0.000000 r=429 88 7 16 121 false 3.361111 11332 11372 A G mi1=336 ma1=30.5k mi2=214 ma2=1.4k pO=0.000000 r=1133 786 27 20 100 false 0.513347 11333 11372 G G mi1=433 ma1=30.4k mi2=214 ma2=1.4k pO=0.000000 r=1167 815 16 14 116 false 0.620321 11331 11372 T G mi1=531 ma1=22.8k mi2=214 ma2=1.4k pO=0.000000 r=1093 577 4 29 128 false 0.902680 11334 11372 T G mi1=542 ma1=30.3k mi2=214 ma2=1.4k pO=0.000000 r=1180 809 12 25 128 false 0.668757 11337 11372 T G mi1=450 ma1=26.3k mi2=214 ma2=1.4k pO=0.000000 r=1237 852 16 22 127 false 0.632470 11338 11372 A G mi1=355 ma1=26.0k mi2=214 ma2=1.4k pO=0.000000 r=1246 847 3 19 115 false 0.614973 11339 11372 C G mi1=303 ma1=26.0k mi2=214 ma2=1.4k pO=0.000000 r=1255 880 11 12 118 false 0.606996 11340 11372 T G mi1=437 ma1=25.8k mi2=214 ma2=1.4k pO=0.000000 r=1269 847 5 37 133 false 0.655172 11342 11372 A G mi1=387 ma1=25.6k mi2=214 ma2=1.4k pO=0.000000 r=1314 889 19 24 126 false 0.593779 11343 11372 T G mi1=449 ma1=25.3k mi2=214 ma2=1.4k pO=0.000000 r=1371 919 2 46 127 false 0.571557 11345 11372 C G mi1=307 ma1=24.6k mi2=214 ma2=1.4k pO=0.000000 r=1401 944 21 11 122 false 0.569030 11347 11372 T G mi1=477 ma1=24.2k mi2=214 ma2=1.4k pO=0.000000 r=1431 946 2 43 138 false 0.612789 11348 11372 A G mi1=346 ma1=24.3k mi2=214 ma2=1.4k pO=0.000000 r=1442 960 25 25 129 false 0.556034 11349 11372 T G mi1=430 ma1=24.1k mi2=214 ma2=1.4k pO=0.000000 r=1451 936 29 58 136 false 0.529595 11350 11372 G G mi1=385 ma1=24.0k mi2=214 ma2=1.4k pO=0.000000 r=1461 956 13 31 124 false 0.547703 11351 11372 A G mi1=364 ma1=23.9k mi2=214 ma2=1.4k pO=0.000000 r=1493 956 6 42 125 false 0.544425 11352 11372 C G mi1=284 ma1=23.2k mi2=214 ma2=1.4k pO=0.000000 r=1533 982 27 26 114 false 0.477387 11353 11372 A G mi1=346 ma1=23.0k mi2=214 ma2=1.4k pO=0.000000 r=1563 994 27 35 120 false 0.483092 11354 11372 G G mi1=387 ma1=22.9k mi2=214 ma2=1.4k pO=0.000000 r=1600 1036 20 13 146 false 0.625000 11355 11372 C G mi1=307 ma1=22.9k mi2=214 ma2=1.4k pO=0.000000 r=1608 1032 17 20 140 false 0.593220 11357 11372 A G mi1=351 ma1=22.9k mi2=214 ma2=1.4k pO=0.000000 r=1664 1100 25 28 123 false 0.468750 11287 11290 - - mi1=23.0k ma1=8.1k mi2=23.0k ma2=7.9k pO=0.000000 r=31389 7839 2 12 22955 false 14.537682 11360 11372 A G mi1=383 ma1=22.6k mi2=214 ma2=1.4k pO=0.000000 r=1701 1106 7 25 139 false 0.563209 11361 11372 C G mi1=258 ma1=22.1k mi2=214 ma2=1.4k pO=0.000000 r=1726 1164 49 11 124 false 0.441595 11362 11372 T G mi1=453 ma1=22.1k mi2=214 ma2=1.4k pO=0.000000 r=1824 1253 23 48 159 false 0.517241 11363 11372 G G mi1=394 ma1=21.7k mi2=214 ma2=1.4k pO=0.000000 r=1826 1245 28 35 158 false 0.527722 11285 11288 - - mi1=23.0k ma1=9.4k mi2=23.0k ma2=8.0k pO=0.000000 r=31390 7868 5 11 22955 false 14.469869 11283 11286 - - mi1=22.9k ma1=9.8k mi2=23.0k ma2=8.0k pO=0.000000 r=31469 7925 25 0 22920 false 14.280374 11365 11372 G G mi1=371 ma1=21.7k mi2=214 ma2=1.4k pO=0.000000 r=1848 1290 27 31 161 false 0.528909 11366 11372 T G mi1=403 ma1=21.0k mi2=214 ma2=1.4k pO=0.000000 r=1861 1295 19 36 160 false 0.528053 11367 11372 A G mi1=326 ma1=21.0k mi2=214 ma2=1.4k pO=0.000000 r=1867 1321 28 24 136 false 0.444735 11368 11372 T G mi1=400 ma1=20.6k mi2=214 ma2=1.4k pO=0.000000 r=1867 1289 30 62 147 false 0.443573 11369 11372 G G mi1=315 ma1=20.4k mi2=214 ma2=1.4k pO=0.000000 r=1881 1322 11 27 140 false 0.474898 11370 11372 A G mi1=362 ma1=20.3k mi2=214 ma2=1.4k pO=0.000000 r=1882 1342 18 24 159 false 0.526490 11371 11372 T G mi1=300 ma1=16.8k mi2=214 ma2=1.4k pO=0.000000 r=1885 1309 6 52 174 false 0.564568 11283 11287 - - mi1=22.9k ma1=9.8k mi2=23.0k ma2=8.1k pO=0.000000 r=31444 7977 25 4 22916 false 14.157914 11364 11372 T G mi1=431 ma1=21.7k mi2=214 ma2=1.4k pO=0.000000 r=1847 1273 29 56 143 false 0.443273 11358 11372 G G mi1=375 ma1=22.8k mi2=214 ma2=1.4k pO=0.000000 r=1687 1104 22 21 146 false 0.572100 11536 11561 A T mi1=554 ma1=1.1k mi2=377 ma2=1.1k pO=0.000000 r=1329 835 31 142 297 false 0.972495 11283 11288 - - mi1=22.9k ma1=9.8k mi2=23.0k ma2=8.0k pO=0.000000 r=31383 7862 25 11 22908 false 14.306770 11335 11372 G G mi1=445 ma1=27.5k mi2=214 ma2=1.4k pO=0.000000 r=1195 824 20 23 123 false 0.617470 11283 11289 - - mi1=22.9k ma1=9.8k mi2=23.0k ma2=8.1k pO=0.000000 r=31378 7916 25 17 22902 false 14.165017 11285 11289 - - mi1=23.0k ma1=9.4k mi2=23.0k ma2=8.1k pO=0.000000 r=31385 7931 5 17 22949 false 14.309141 11283 11290 - - mi1=22.9k ma1=9.8k mi2=23.0k ma2=7.9k pO=0.000000 r=31358 7830 26 12 22902 false 14.346029 11285 11290 - - mi1=23.0k ma1=9.4k mi2=23.0k ma2=7.9k pO=0.000000 r=31365 7812 7 12 22949 false 14.546780 14211 14271 T A mi1=298 ma1=15.5k mi2=216 ma2=929 pO=0.000000 r=241 24 8 10 108 false 5.625000 14222 14271 T A mi1=271 ma1=13.8k mi2=216 ma2=929 pO=0.000000 r=285 26 13 20 113 false 3.575949 14224 14271 A A mi1=239 ma1=13.6k mi2=216 ma2=929 pO=0.000000 r=290 24 10 11 104 false 4.814815 14228 14271 A A mi1=225 ma1=12.7k mi2=216 ma2=929 pO=0.000000 r=319 33 9 12 102 false 4.358974 14231 14271 C A mi1=222 ma1=12.3k mi2=216 ma2=929 pO=0.000000 r=335 31 27 12 104 false 2.780749 14233 14271 T A mi1=289 ma1=14.6k mi2=216 ma2=929 pO=0.000000 r=914 599 24 24 106 false 0.670038 14236 14271 A A mi1=240 ma1=14.5k mi2=216 ma2=929 pO=0.000000 r=970 639 21 7 100 false 0.665779 14238 14271 T A mi1=248 ma1=13.4k mi2=216 ma2=929 pO=0.000000 r=999 642 29 33 111 false 0.623596 14240 14271 A A mi1=234 ma1=13.3k mi2=216 ma2=929 pO=0.000000 r=1026 647 13 10 121 false 0.818674 14242 14271 T A mi1=273 ma1=12.9k mi2=216 ma2=929 pO=0.000000 r=1039 649 20 17 128 false 0.803011 14245 14271 G A mi1=179 ma1=12.6k mi2=216 ma2=929 pO=0.000000 r=1082 668 44 13 104 false 0.580357 14246 14271 A A mi1=231 ma1=12.6k mi2=216 ma2=929 pO=0.000000 r=1089 656 44 14 106 false 0.596847 14249 14271 T A mi1=281 ma1=12.3k mi2=216 ma2=929 pO=0.000000 r=1140 683 16 28 132 false 0.768335 14252 14271 T A mi1=258 ma1=12.2k mi2=216 ma2=929 pO=0.000000 r=1188 717 41 25 126 false 0.642202 14256 14271 A A mi1=251 ma1=12.1k mi2=216 ma2=929 pO=0.000000 r=1265 779 41 15 128 false 0.638086 14257 14271 T A mi1=269 ma1=12.1k mi2=216 ma2=929 pO=0.000000 r=1267 776 40 16 121 false 0.605000 14258 14271 A A mi1=239 ma1=11.9k mi2=216 ma2=929 pO=0.000000 r=1268 776 51 22 137 false 0.641386 14259 14271 T A mi1=263 ma1=11.7k mi2=216 ma2=929 pO=0.000000 r=1272 777 12 40 118 false 0.598985 14261 14271 A A mi1=227 ma1=11.6k mi2=216 ma2=929 pO=0.000000 r=1310 816 18 24 111 false 0.564024 14262 14271 C A mi1=162 ma1=11.3k mi2=216 ma2=929 pO=0.000000 r=1313 819 65 13 106 false 0.468612 14264 14271 T A mi1=278 ma1=11.0k mi2=216 ma2=929 pO=0.000000 r=1327 814 22 35 132 false 0.633397 14266 14271 A A mi1=246 ma1=11.0k mi2=216 ma2=929 pO=0.000000 r=1341 833 34 37 111 false 0.496867 14267 14271 C A mi1=154 ma1=11.0k mi2=216 ma2=929 pO=0.000000 r=1342 831 31 25 106 false 0.502370 14269 14271 G A mi1=183 ma1=10.8k mi2=216 ma2=929 pO=0.000000 r=1376 883 27 12 100 false 0.481232 14241 14271 G A mi1=187 ma1=13.2k mi2=216 ma2=929 pO=0.000000 r=1030 650 25 5 104 false 0.675325 14819 14898 T C mi1=331 ma1=20.3k mi2=186 ma2=193 pO=0.000000 r=170 7 0 3 100 false 26.315789 14824 14898 A C mi1=339 ma1=20.4k mi2=186 ma2=193 pO=0.000000 r=181 9 1 4 101 false 17.413793 14827 14898 A C mi1=344 ma1=20.0k mi2=186 ma2=193 pO=0.000000 r=189 15 0 7 102 false 11.860465 14828 14898 T C mi1=334 ma1=20.3k mi2=186 ma2=193 pO=0.000000 r=194 7 1 6 103 false 14.714286 14829 14898 G C mi1=301 ma1=20.2k mi2=186 ma2=193 pO=0.000000 r=203 10 2 3 106 false 17.666667 14830 14898 T C mi1=363 ma1=20.2k mi2=186 ma2=193 pO=0.000000 r=204 5 2 17 102 false 6.296296 14831 14898 G C mi1=273 ma1=20.2k mi2=186 ma2=193 pO=0.000000 r=209 14 5 5 103 false 9.537037 14832 14898 T C mi1=351 ma1=20.1k mi2=186 ma2=193 pO=0.000000 r=211 7 5 14 103 false 6.204819 14833 14898 G C mi1=277 ma1=20.2k mi2=186 ma2=193 pO=0.000000 r=216 8 2 3 107 false 19.107143 14834 14898 A C mi1=317 ma1=20.2k mi2=186 ma2=193 pO=0.000000 r=221 16 7 11 109 false 6.193182 14835 14898 T C mi1=346 ma1=20.0k mi2=186 ma2=193 pO=0.000000 r=226 19 1 7 112 false 10.980392 14836 14898 A C mi1=310 ma1=20.0k mi2=186 ma2=193 pO=0.000000 r=228 14 0 3 109 false 20.961538 14837 14898 T C mi1=340 ma1=19.2k mi2=186 ma2=193 pO=0.000000 r=234 10 1 11 116 false 10.000000 14838 14898 C C mi1=264 ma1=19.1k mi2=186 ma2=193 pO=0.000000 r=234 16 2 9 109 false 9.083333 14839 14898 A C mi1=307 ma1=19.2k mi2=186 ma2=193 pO=0.000000 r=236 7 0 10 111 false 11.808511 14840 14898 G C mi1=255 ma1=19.1k mi2=186 ma2=193 pO=0.000000 r=243 15 2 8 111 false 10.090909 14841 14898 A C mi1=308 ma1=19.1k mi2=186 ma2=193 pO=0.000000 r=248 13 1 11 114 false 9.344262 14842 14898 C C mi1=266 ma1=18.6k mi2=186 ma2=193 pO=0.000000 r=256 18 0 12 115 false 8.712121 14845 14898 C C mi1=265 ma1=18.7k mi2=186 ma2=193 pO=0.000000 r=273 32 7 8 118 false 6.413043 14847 14898 A C mi1=318 ma1=18.6k mi2=186 ma2=193 pO=0.000000 r=290 19 0 21 125 false 6.067961 14846 14898 T C mi1=322 ma1=18.8k mi2=186 ma2=193 pO=0.000000 r=275 17 0 21 125 false 6.188119 14844 14898 A C mi1=337 ma1=18.7k mi2=186 ma2=193 pO=0.000000 r=260 10 1 15 118 false 7.972973 14848 14898 C C mi1=261 ma1=18.4k mi2=186 ma2=193 pO=0.000000 r=300 37 1 8 126 false 8.630137 14849 14898 T C mi1=354 ma1=18.4k mi2=186 ma2=193 pO=0.000000 r=308 14 0 25 135 false 5.921053 14850 14898 A C mi1=310 ma1=18.1k mi2=186 ma2=193 pO=0.000000 r=315 31 6 21 123 false 4.424460 14853 14898 T C mi1=359 ma1=17.4k mi2=186 ma2=193 pO=0.000000 r=333 22 10 16 129 false 5.119048 14854 14898 G C mi1=229 ma1=17.5k mi2=186 ma2=193 pO=0.000000 r=334 34 7 4 125 false 8.012821 14855 14898 T C mi1=293 ma1=17.0k mi2=186 ma2=193 pO=0.000000 r=339 24 6 30 132 false 3.928571 14856 14898 A C mi1=261 ma1=17.0k mi2=186 ma2=193 pO=0.000000 r=342 26 11 20 123 false 4.100000 14857 14898 G C mi1=239 ma1=16.9k mi2=186 ma2=193 pO=0.000000 r=347 39 6 17 126 false 4.809160 14859 14898 T C mi1=325 ma1=16.0k mi2=186 ma2=193 pO=0.000000 r=357 27 0 26 127 false 4.847328 14860 14898 G C mi1=246 ma1=16.1k mi2=186 ma2=193 pO=0.000000 r=365 24 16 24 127 false 3.451087 14862 14898 A C mi1=309 ma1=16.0k mi2=186 ma2=193 pO=0.000000 r=382 38 14 14 126 false 4.200000 14863 14898 G C mi1=245 ma1=15.9k mi2=186 ma2=193 pO=0.000000 r=389 33 7 24 130 false 4.140127 14865 14898 T C mi1=343 ma1=15.5k mi2=186 ma2=193 pO=0.000000 r=406 17 16 37 135 false 2.947598 14866 14898 G C mi1=240 ma1=15.5k mi2=186 ma2=193 pO=0.000000 r=413 38 7 24 136 false 4.197531 14868 14898 T C mi1=360 ma1=15.3k mi2=186 ma2=193 pO=0.000000 r=431 35 7 48 128 false 2.509804 14869 14898 G C mi1=242 ma1=15.3k mi2=186 ma2=193 pO=0.000000 r=436 40 14 31 129 false 2.931818 14870 14898 A C mi1=271 ma1=15.3k mi2=186 ma2=193 pO=0.000000 r=445 44 29 31 131 false 2.306338 14871 14898 T C mi1=330 ma1=15.1k mi2=186 ma2=193 pO=0.000000 r=453 26 12 45 140 false 2.755906 14873 14898 A C mi1=299 ma1=15.0k mi2=186 ma2=193 pO=0.000000 r=467 25 6 22 132 false 4.817518 14874 14898 G C mi1=234 ma1=14.7k mi2=186 ma2=193 pO=0.000000 r=472 50 20 18 140 false 3.465347 14875 14898 T C mi1=313 ma1=14.6k mi2=186 ma2=193 pO=0.000000 r=481 52 11 29 129 false 3.042453 14876 14898 A C mi1=291 ma1=14.5k mi2=186 ma2=193 pO=0.000000 r=490 35 8 23 145 false 4.559748 14877 14898 C C mi1=217 ma1=13.9k mi2=186 ma2=193 pO=0.000000 r=499 50 23 25 126 false 2.603306 14880 14898 T C mi1=311 ma1=13.7k mi2=186 ma2=193 pO=0.000000 r=521 39 12 45 147 false 2.752809 14881 14898 G C mi1=241 ma1=13.6k mi2=186 ma2=193 pO=0.000000 r=522 57 6 25 158 false 4.364641 14882 14898 A C mi1=254 ma1=13.3k mi2=186 ma2=193 pO=0.000000 r=525 75 6 33 135 false 2.922078 14885 14898 G C mi1=219 ma1=12.7k mi2=186 ma2=193 pO=0.000000 r=535 46 26 13 134 false 3.316832 14891 14898 A C mi1=255 ma1=12.3k mi2=186 ma2=193 pO=0.000000 r=551 46 7 54 139 false 2.396552 14890 14898 G C mi1=230 ma1=12.3k mi2=186 ma2=193 pO=0.000000 r=551 60 11 28 156 false 3.611111 14889 14898 C C mi1=212 ma1=12.3k mi2=186 ma2=193 pO=0.000000 r=551 42 13 27 135 false 3.341584 14887 14898 T C mi1=313 ma1=12.6k mi2=186 ma2=193 pO=0.000000 r=544 47 33 46 132 false 1.818182 14888 14898 A C mi1=270 ma1=12.5k mi2=186 ma2=193 pO=0.000000 r=546 46 11 64 135 false 1.950867 14892 14898 T C mi1=291 ma1=12.1k mi2=186 ma2=193 pO=0.000000 r=551 21 7 60 169 false 2.923875 14894 14898 G C mi1=208 ma1=11.3k mi2=186 ma2=193 pO=0.000000 r=551 44 15 31 125 false 2.741228 14895 14898 T C mi1=283 ma1=11.3k mi2=186 ma2=193 pO=0.000000 r=596 64 3 71 152 false 2.111111 14897 14898 G C mi1=227 ma1=11.2k mi2=186 ma2=193 pO=0.000000 r=601 92 2 25 141 false 3.525000 14884 14898 T C mi1=319 ma1=12.8k mi2=186 ma2=193 pO=0.000000 r=534 62 14 34 136 false 2.677165 15459 15538 A G mi1=369 ma1=21.6k mi2=227 ma2=839 pO=0.000000 r=171 28 1 3 101 false 11.477273 15462 15538 T G mi1=413 ma1=21.6k mi2=227 ma2=839 pO=0.000000 r=185 17 0 6 107 false 13.048780 15463 15538 G G mi1=356 ma1=21.5k mi2=227 ma2=839 pO=0.000000 r=188 28 2 4 106 false 10.192308 15461 15538 A G mi1=376 ma1=21.9k mi2=227 ma2=839 pO=0.000000 r=178 29 2 2 103 false 11.444444 15468 15538 A G mi1=370 ma1=20.0k mi2=227 ma2=839 pO=0.000000 r=206 15 0 14 109 false 7.676056 15465 15538 T G mi1=413 ma1=20.1k mi2=227 ma2=839 pO=0.000000 r=199 14 4 22 107 false 4.533898 15470 15538 C G mi1=294 ma1=18.8k mi2=227 ma2=839 pO=0.000000 r=212 17 6 11 109 false 6.411765 15471 15538 A G mi1=343 ma1=18.9k mi2=227 ma2=839 pO=0.000000 r=216 19 2 1 114 false 18.387097 15474 15538 T G mi1=362 ma1=18.7k mi2=227 ma2=839 pO=0.000000 r=227 29 6 9 116 false 6.516854 15476 15538 G G mi1=361 ma1=18.7k mi2=227 ma2=839 pO=0.000000 r=237 19 7 13 114 false 5.757576 15473 15538 G G mi1=351 ma1=18.8k mi2=227 ma2=839 pO=0.000000 r=223 18 7 15 109 false 5.141509 15478 15538 A G mi1=379 ma1=18.5k mi2=227 ma2=839 pO=0.000000 r=249 19 0 28 114 false 4.351145 15480 15538 C G mi1=313 ma1=18.0k mi2=227 ma2=839 pO=0.000000 r=265 24 6 21 113 false 4.280303 15483 15538 A G mi1=330 ma1=18.0k mi2=227 ma2=839 pO=0.000000 r=271 21 19 22 112 false 3.027027 15482 15538 C G mi1=313 ma1=17.9k mi2=227 ma2=839 pO=0.000000 r=270 30 0 0 123 false 20.500000 15481 15538 T G mi1=365 ma1=17.9k mi2=227 ma2=839 pO=0.000000 r=267 33 1 22 119 false 4.760000 15484 15538 T G mi1=353 ma1=17.8k mi2=227 ma2=839 pO=0.000000 r=273 17 8 19 115 false 4.600000 15485 15538 C G mi1=299 ma1=17.7k mi2=227 ma2=839 pO=0.000000 r=279 24 13 13 117 false 4.570313 15486 15538 A G mi1=333 ma1=17.6k mi2=227 ma2=839 pO=0.000000 r=281 26 1 14 122 false 7.093023 15490 15538 G G mi1=296 ma1=15.8k mi2=227 ma2=839 pO=0.000000 r=298 43 0 18 117 false 5.086957 15488 15538 G G mi1=348 ma1=17.0k mi2=227 ma2=839 pO=0.000000 r=288 35 13 20 117 false 3.502994 15492 15538 T G mi1=324 ma1=15.5k mi2=227 ma2=839 pO=0.000000 r=312 42 9 9 121 false 5.307018 15491 15538 A G mi1=323 ma1=15.6k mi2=227 ma2=839 pO=0.000000 r=310 35 17 14 118 false 3.710692 15493 15538 G G mi1=319 ma1=15.4k mi2=227 ma2=839 pO=0.000000 r=326 22 10 6 129 false 7.500000 15496 15538 A G mi1=326 ma1=15.1k mi2=227 ma2=839 pO=0.000000 r=341 34 7 20 128 false 4.507042 15489 15538 A G mi1=320 ma1=17.0k mi2=227 ma2=839 pO=0.000000 r=293 39 9 14 124 false 4.732824 15497 15538 C G mi1=269 ma1=15.1k mi2=227 ma2=839 pO=0.000000 r=346 42 27 15 114 false 2.714286 15500 15538 C G mi1=245 ma1=14.0k mi2=227 ma2=839 pO=0.000000 r=358 42 24 5 115 false 3.639241 15495 15538 C G mi1=275 ma1=15.1k mi2=227 ma2=839 pO=0.000000 r=337 35 12 24 112 false 3.128492 15502 15538 G G mi1=327 ma1=13.6k mi2=227 ma2=839 pO=0.000000 r=371 25 0 26 129 false 5.000000 15503 15538 C G mi1=242 ma1=15.3k mi2=227 ma2=839 pO=0.000000 r=777 441 34 7 115 false 0.950413 15499 15538 A G mi1=358 ma1=15.0k mi2=227 ma2=839 pO=0.000000 r=353 34 7 36 136 false 3.300971 15507 15538 T G mi1=337 ma1=15.1k mi2=227 ma2=839 pO=0.000000 r=937 562 7 10 143 false 1.134921 15508 15538 G G mi1=329 ma1=14.8k mi2=227 ma2=839 pO=0.000000 r=966 552 4 13 150 false 1.209677 15501 15538 T G mi1=312 ma1=13.9k mi2=227 ma2=839 pO=0.000000 r=363 33 10 25 124 false 3.583815 15506 15538 A G mi1=321 ma1=15.3k mi2=227 ma2=839 pO=0.000000 r=919 558 27 30 114 false 0.725191 15505 15538 T G mi1=349 ma1=15.0k mi2=227 ma2=839 pO=0.000000 r=805 435 20 50 124 false 0.867133 15512 15538 A G mi1=315 ma1=13.8k mi2=227 ma2=839 pO=0.000000 r=1016 592 24 33 141 false 0.859756 15509 15538 C G mi1=245 ma1=14.7k mi2=227 ma2=839 pO=0.000000 r=977 573 23 5 121 false 0.883212 15510 15538 T G mi1=301 ma1=13.9k mi2=227 ma2=839 pO=0.000000 r=985 579 16 47 148 false 0.890493 15513 15538 T G mi1=314 ma1=13.7k mi2=227 ma2=839 pO=0.000000 r=1029 597 15 27 148 false 0.967320 15514 15538 A G mi1=297 ma1=13.7k mi2=227 ma2=839 pO=0.000000 r=1038 576 30 34 147 false 0.883413 15517 15538 G G mi1=276 ma1=12.0k mi2=227 ma2=839 pO=0.000000 r=1088 635 38 35 141 false 0.760518 15516 15538 T G mi1=310 ma1=12.3k mi2=227 ma2=839 pO=0.000000 r=1081 618 19 37 141 false 0.837292 15515 15538 G G mi1=276 ma1=12.4k mi2=227 ma2=839 pO=0.000000 r=1049 591 26 21 153 false 0.982028 15522 15538 T G mi1=314 ma1=11.6k mi2=227 ma2=839 pO=0.000000 r=1149 639 54 32 163 false 0.829095 15524 15538 A G mi1=297 ma1=11.5k mi2=227 ma2=839 pO=0.000000 r=1160 625 5 38 149 false 0.934755 15525 15538 C G mi1=204 ma1=11.2k mi2=227 ma2=839 pO=0.000000 r=1160 650 25 28 127 false 0.736659 15526 15538 A G mi1=294 ma1=11.1k mi2=227 ma2=839 pO=0.000000 r=1161 664 37 17 144 false 0.818182 15529 15538 T G mi1=303 ma1=10.7k mi2=227 ma2=839 pO=0.000000 r=1185 689 23 44 165 false 0.862069 15530 15538 G G mi1=293 ma1=10.7k mi2=227 ma2=839 pO=0.000000 r=1187 697 19 48 157 false 0.813472 15531 15538 T G mi1=318 ma1=10.6k mi2=227 ma2=839 pO=0.000000 r=1188 666 9 52 165 false 0.906593 15532 15538 C G mi1=191 ma1=10.6k mi2=227 ma2=839 pO=0.000000 r=1194 699 19 12 137 false 0.832321 15534 15538 A G mi1=273 ma1=10.4k mi2=227 ma2=839 pO=0.000000 r=1200 684 15 48 172 false 0.918803 15537 15538 T G mi1=243 ma1=9.8k mi2=227 ma2=839 pO=0.000000 r=1249 745 22 31 170 false 0.888192 15536 15538 C G mi1=201 ma1=9.9k mi2=227 ma2=839 pO=0.000000 r=1202 692 16 18 142 false 0.857488 15535 15538 G G mi1=247 ma1=10.2k mi2=227 ma2=839 pO=0.000000 r=1202 679 32 22 145 false 0.810056 17288 17430 C C mi1=472 ma1=44.3k mi2=274 ma2=859 pO=0.000000 r=125 11 1 0 108 false 36.000000 17289 17430 A C mi1=542 ma1=44.8k mi2=274 ma2=859 pO=0.000000 r=127 0 0 0 110 false Infinity 17291 17430 T C mi1=645 ma1=44.4k mi2=274 ma2=859 pO=0.000000 r=132 0 0 12 114 false 11.875000 17295 17430 A C mi1=647 ma1=43.2k mi2=274 ma2=859 pO=0.000000 r=147 0 0 15 126 false 10.500000 17292 17430 A C mi1=582 ma1=44.6k mi2=274 ma2=859 pO=0.000000 r=133 0 0 0 115 false Infinity 17293 17430 G C mi1=532 ma1=45.5k mi2=274 ma2=859 pO=0.000000 r=134 12 0 0 115 false 47.916667 17298 17430 G C mi1=511 ma1=41.0k mi2=274 ma2=859 pO=0.000000 r=153 0 0 0 130 false Infinity 17297 17430 A C mi1=565 ma1=41.7k mi2=274 ma2=859 pO=0.000000 r=152 1 0 1 128 false 128.000000 17300 17430 A C mi1=592 ma1=41.0k mi2=274 ma2=859 pO=0.000000 r=162 18 0 0 138 false 38.333333 17301 17430 T C mi1=586 ma1=41.2k mi2=274 ma2=859 pO=0.000000 r=163 0 0 1 137 false 171.250000 17302 17430 G C mi1=547 ma1=41.3k mi2=274 ma2=859 pO=0.000000 r=166 17 0 0 140 false 41.176471 17299 17430 T C mi1=610 ma1=41.0k mi2=274 ma2=859 pO=0.000000 r=161 1 0 0 138 false 690.000000 17303 17430 T C mi1=585 ma1=42.4k mi2=274 ma2=859 pO=0.000000 r=166 0 0 0 139 false Infinity 17296 17430 C C mi1=447 ma1=41.3k mi2=274 ma2=859 pO=0.000000 r=149 16 0 0 127 false 39.687500 17304 17430 C C mi1=481 ma1=41.9k mi2=274 ma2=859 pO=0.000000 r=170 17 0 0 140 false 41.176471 17308 17430 T C mi1=640 ma1=41.2k mi2=274 ma2=859 pO=0.000000 r=178 4 0 18 142 false 9.342105 17309 17430 G C mi1=507 ma1=41.3k mi2=274 ma2=859 pO=0.000000 r=179 22 0 0 143 false 32.500000 17310 17430 T C mi1=563 ma1=40.5k mi2=274 ma2=859 pO=0.000000 r=187 13 0 0 143 false 55.000000 17311 17430 A C mi1=566 ma1=41.0k mi2=274 ma2=859 pO=0.000000 r=190 12 0 1 143 false 44.687500 17312 17430 C C mi1=452 ma1=39.6k mi2=274 ma2=859 pO=0.000000 r=194 13 0 1 147 false 43.235294 17314 17430 G C mi1=474 ma1=40.9k mi2=274 ma2=859 pO=0.000000 r=214 44 1 1 153 false 14.711538 17318 17430 A C mi1=657 ma1=41.0k mi2=274 ma2=859 pO=0.000000 r=222 29 0 23 154 false 6.363636 17315 17430 T C mi1=596 ma1=40.9k mi2=274 ma2=859 pO=0.000000 r=217 26 0 2 154 false 22.647059 17313 17430 T C mi1=541 ma1=40.9k mi2=274 ma2=859 pO=0.000000 r=207 24 0 1 147 false 26.250000 17321 17430 C C mi1=427 ma1=39.4k mi2=274 ma2=859 pO=0.000000 r=228 31 1 0 155 false 22.142857 17319 17430 T C mi1=591 ma1=40.9k mi2=274 ma2=859 pO=0.000000 r=225 30 0 0 154 false 25.666667 17320 17430 G C mi1=472 ma1=40.1k mi2=274 ma2=859 pO=0.000000 r=225 29 0 0 154 false 26.551724 17325 17430 G C mi1=479 ma1=38.4k mi2=274 ma2=859 pO=0.000000 r=254 31 0 0 161 false 25.967742 17324 17430 T C mi1=605 ma1=38.2k mi2=274 ma2=859 pO=0.000000 r=243 31 0 22 155 false 6.512605 17322 17430 A C mi1=528 ma1=38.8k mi2=274 ma2=859 pO=0.000000 r=232 29 0 0 156 false 26.896552 17327 17430 C C mi1=499 ma1=38.0k mi2=274 ma2=859 pO=0.000000 r=274 37 0 24 161 false 6.052632 17329 17430 G C mi1=474 ma1=37.9k mi2=274 ma2=859 pO=0.000000 r=284 35 0 0 163 false 23.285714 17332 17430 A C mi1=590 ma1=37.5k mi2=274 ma2=859 pO=0.000000 r=291 36 0 3 161 false 16.770833 17330 17430 A C mi1=550 ma1=38.1k mi2=274 ma2=859 pO=0.000000 r=285 61 0 4 162 false 10.519481 17331 17430 G C mi1=485 ma1=37.9k mi2=274 ma2=859 pO=0.000000 r=289 60 0 0 162 false 13.500000 17328 17430 T C mi1=570 ma1=37.9k mi2=274 ma2=859 pO=0.000000 r=281 35 0 1 163 false 20.897436 17334 17430 G C mi1=465 ma1=35.3k mi2=274 ma2=859 pO=0.000000 r=297 36 0 5 161 false 14.375000 17333 17430 C C mi1=427 ma1=35.9k mi2=274 ma2=859 pO=0.000000 r=294 37 0 1 162 false 19.756098 17337 17430 A C mi1=551 ma1=35.7k mi2=274 ma2=859 pO=0.000000 r=310 41 0 1 163 false 18.111111 17336 17430 C C mi1=424 ma1=35.4k mi2=274 ma2=859 pO=0.000000 r=303 68 0 3 163 false 10.187500 17335 17430 A C mi1=550 ma1=35.3k mi2=274 ma2=859 pO=0.000000 r=301 36 0 9 162 false 11.250000 17338 17430 G C mi1=471 ma1=36.1k mi2=274 ma2=859 pO=0.000000 r=321 47 0 1 163 false 15.980392 17339 17430 C C mi1=444 ma1=36.3k mi2=274 ma2=859 pO=0.000000 r=326 50 0 1 166 false 15.370370 17341 17430 G C mi1=480 ma1=37.5k mi2=274 ma2=859 pO=0.000000 r=347 90 2 3 173 false 7.863636 17344 17430 A C mi1=575 ma1=37.6k mi2=274 ma2=859 pO=0.000000 r=368 90 0 7 187 false 7.923729 17343 17430 T C mi1=589 ma1=37.5k mi2=274 ma2=859 pO=0.000000 r=360 90 4 4 177 false 7.254098 17340 17430 A C mi1=543 ma1=36.8k mi2=274 ma2=859 pO=0.000000 r=334 49 0 6 167 false 11.438356 17346 17430 A C mi1=591 ma1=37.3k mi2=274 ma2=859 pO=0.000000 r=380 57 0 10 181 false 9.329897 17345 17430 T C mi1=616 ma1=37.4k mi2=274 ma2=859 pO=0.000000 r=375 86 4 3 181 false 7.938596 17342 17430 A C mi1=582 ma1=37.5k mi2=274 ma2=859 pO=0.000000 r=355 60 2 5 178 false 10.113636 17349 17430 T C mi1=603 ma1=35.6k mi2=274 ma2=859 pO=0.000000 r=391 58 1 35 180 false 4.455446 17347 17430 G C mi1=492 ma1=36.6k mi2=274 ma2=859 pO=0.000000 r=383 65 3 7 182 false 8.666667 17350 17430 G C mi1=468 ma1=34.7k mi2=274 ma2=859 pO=0.000000 r=396 88 2 10 182 false 6.691176 17356 17430 G C mi1=470 ma1=34.2k mi2=274 ma2=859 pO=0.000000 r=421 73 2 3 185 false 9.946237 17357 17430 A C mi1=533 ma1=34.2k mi2=274 ma2=859 pO=0.000000 r=426 76 4 16 185 false 5.929487 17358 17430 T C mi1=554 ma1=34.1k mi2=274 ma2=859 pO=0.000000 r=430 74 6 7 187 false 7.420635 17359 17430 G C mi1=483 ma1=34.1k mi2=274 ma2=859 pO=0.000000 r=439 86 5 1 181 false 8.227273 17351 17430 T C mi1=526 ma1=34.5k mi2=274 ma2=859 pO=0.000000 r=406 64 2 10 182 false 8.125000 17355 17430 T C mi1=596 ma1=34.1k mi2=274 ma2=859 pO=0.000000 r=419 79 2 40 184 false 3.724696 17362 17430 A C mi1=610 ma1=34.1k mi2=274 ma2=859 pO=0.000000 r=446 81 6 39 184 false 3.524904 17365 17430 T C mi1=614 ma1=33.5k mi2=274 ma2=859 pO=0.000000 r=460 74 0 45 192 false 3.779528 17366 17430 C C mi1=459 ma1=33.6k mi2=274 ma2=859 pO=0.000000 r=466 76 5 10 185 false 6.801471 17368 17430 A C mi1=599 ma1=33.5k mi2=274 ma2=859 pO=0.000000 r=477 87 8 40 184 false 3.297491 17369 17430 T C mi1=578 ma1=33.3k mi2=274 ma2=859 pO=0.000000 r=481 76 4 29 183 false 4.399038 17371 17430 G C mi1=549 ma1=33.1k mi2=274 ma2=859 pO=0.000000 r=497 76 0 42 184 false 3.770492 17373 17430 C C mi1=516 ma1=33.1k mi2=274 ma2=859 pO=0.000000 r=509 101 13 38 181 false 2.967213 17374 17430 A C mi1=572 ma1=33.1k mi2=274 ma2=859 pO=0.000000 r=515 129 0 10 187 false 5.532544 17375 17430 C C mi1=473 ma1=33.2k mi2=274 ma2=859 pO=0.000000 r=522 113 10 10 181 false 4.689119 17378 17430 A C mi1=688 ma1=32.5k mi2=274 ma2=859 pO=0.000000 r=542 98 14 55 183 false 2.446524 17380 17430 T C mi1=671 ma1=32.0k mi2=274 ma2=859 pO=0.000000 r=552 96 7 49 191 false 2.984375 17382 17430 T C mi1=633 ma1=31.8k mi2=274 ma2=859 pO=0.000000 r=570 107 2 14 200 false 5.847953 17383 17430 G C mi1=520 ma1=31.7k mi2=274 ma2=859 pO=0.000000 r=571 100 2 28 197 false 4.477273 17384 17430 A C mi1=661 ma1=31.5k mi2=274 ma2=859 pO=0.000000 r=579 100 6 36 190 false 3.544776 17387 17430 T C mi1=663 ma1=30.7k mi2=274 ma2=859 pO=0.000000 r=604 106 4 47 197 false 3.177419 17388 17430 G C mi1=498 ma1=30.7k mi2=274 ma2=859 pO=0.000000 r=626 100 18 34 187 false 3.035714 17389 17430 A C mi1=626 ma1=30.5k mi2=274 ma2=859 pO=0.000000 r=642 110 16 30 208 false 3.537415 17390 17430 G C mi1=547 ma1=30.4k mi2=274 ma2=859 pO=0.000000 r=660 101 8 20 187 false 4.389671 17391 17430 T C mi1=648 ma1=30.1k mi2=274 ma2=859 pO=0.000000 r=681 133 4 25 195 false 3.915663 17392 17430 G C mi1=511 ma1=30.0k mi2=274 ma2=859 pO=0.000000 r=697 146 11 12 194 false 4.075630 17394 17430 T C mi1=692 ma1=29.3k mi2=274 ma2=859 pO=0.000000 r=722 99 0 69 221 false 2.946667 17395 17430 G C mi1=527 ma1=29.4k mi2=274 ma2=859 pO=0.000000 r=737 134 24 19 190 false 3.104575 17397 17430 C C mi1=490 ma1=28.5k mi2=274 ma2=859 pO=0.000000 r=778 108 27 22 201 false 3.305921 17396 17430 T C mi1=695 ma1=28.7k mi2=274 ma2=859 pO=0.000000 r=762 107 4 58 197 false 2.774648 17399 17430 A C mi1=763 ma1=27.4k mi2=274 ma2=859 pO=0.000000 r=817 127 20 70 220 false 2.258727 17400 17430 T C mi1=659 ma1=27.0k mi2=274 ma2=859 pO=0.000000 r=841 112 3 33 214 false 4.179688 17401 17430 G C mi1=514 ma1=26.9k mi2=274 ma2=859 pO=0.000000 r=860 109 3 26 198 false 4.400000 17403 17430 C C mi1=499 ma1=26.3k mi2=274 ma2=859 pO=0.000000 r=888 137 37 34 191 false 2.268409 17405 17430 G C mi1=523 ma1=26.3k mi2=274 ma2=859 pO=0.000000 r=908 158 8 30 217 false 3.500000 17406 17430 A C mi1=648 ma1=26.4k mi2=274 ma2=859 pO=0.000000 r=1105 313 43 76 201 false 1.273764 17408 17430 T C mi1=697 ma1=25.7k mi2=274 ma2=859 pO=0.000000 r=1138 383 12 64 224 false 1.630277 17409 17430 A C mi1=632 ma1=25.3k mi2=274 ma2=859 pO=0.000000 r=1147 316 7 89 209 false 1.492857 17410 17430 C C mi1=460 ma1=25.4k mi2=274 ma2=859 pO=0.000000 r=1186 358 8 26 192 false 1.943320 17411 17430 G C mi1=515 ma1=25.5k mi2=274 ma2=859 pO=0.000000 r=1190 387 51 58 212 false 1.287971 17412 17430 T C mi1=730 ma1=25.3k mi2=274 ma2=859 pO=0.000000 r=1266 465 17 61 244 false 1.570142 17413 17430 G C mi1=543 ma1=25.0k mi2=274 ma2=859 pO=0.000000 r=1270 399 13 17 212 false 2.042389 17412 17430 T T mi1=730 ma1=25.3k mi2=232 ma2=859 pO=0.000000 r=1266 465 17 61 101 false 0.649936 17414 17430 C C mi1=417 ma1=24.8k mi2=274 ma2=859 pO=0.000000 r=1270 471 47 23 185 false 1.231691 17404 17430 A C mi1=659 ma1=26.1k mi2=274 ma2=859 pO=0.000000 r=896 110 9 42 237 false 3.773885 17415 17430 T C mi1=699 ma1=24.6k mi2=274 ma2=859 pO=0.000000 r=1279 423 37 89 213 false 1.148867 17416 17430 T T mi1=451 ma1=24.9k mi2=232 ma2=859 pO=0.000000 r=1284 432 27 111 127 false 0.645325 17417 17430 A C mi1=579 ma1=24.5k mi2=274 ma2=859 pO=0.000000 r=1339 480 27 66 200 false 1.173709 17418 17430 G C mi1=492 ma1=24.3k mi2=274 ma2=859 pO=0.000000 r=1343 488 5 20 221 false 1.879252 17419 17430 C C mi1=419 ma1=23.7k mi2=274 ma2=859 pO=0.000000 r=1346 502 31 21 185 false 1.302817 17420 17430 A C mi1=534 ma1=23.6k mi2=274 ma2=859 pO=0.000000 r=1384 549 2 33 241 false 1.748911 17421 17430 C C mi1=392 ma1=22.1k mi2=274 ma2=859 pO=0.000000 r=1386 610 20 30 206 false 1.271605 17422 17430 T C mi1=639 ma1=22.0k mi2=274 ma2=859 pO=0.000000 r=1443 583 32 68 229 false 1.164802 17424 17430 T C mi1=599 ma1=21.8k mi2=274 ma2=859 pO=0.000000 r=1497 652 22 43 208 false 1.140351 17425 17430 G C mi1=454 ma1=21.1k mi2=274 ma2=859 pO=0.000000 r=1499 682 3 13 202 false 1.353887 17426 17430 T C mi1=496 ma1=19.0k mi2=274 ma2=859 pO=0.000000 r=1511 692 8 67 208 false 1.048387 17427 17430 G C mi1=359 ma1=18.6k mi2=274 ma2=859 pO=0.000000 r=1517 746 58 53 190 false 0.798319 17428 17430 T C mi1=488 ma1=18.4k mi2=274 ma2=859 pO=0.000000 r=1522 682 3 70 226 false 1.160164 17429 17430 A C mi1=444 ma1=18.2k mi2=274 ma2=859 pO=0.000000 r=1525 677 24 75 198 false 0.922647 17429 17430 T G mi1=286 ma1=18.2k mi2=160 ma2=859 pO=0.000000 r=1525 677 5 67 113 false 0.585492 17352 17430 C C mi1=465 ma1=34.5k mi2=274 ma2=859 pO=0.000000 r=409 104 1 2 182 false 7.844828 17423 17430 A C mi1=521 ma1=22.1k mi2=274 ma2=859 pO=0.000000 r=1447 668 33 63 195 false 0.926806 17381 17430 A C mi1=618 ma1=32.0k mi2=274 ma2=859 pO=0.000000 r=566 128 17 34 189 false 2.846386 18566 18650 A A mi1=428 ma1=25.2k mi2=331 ma2=822 pO=0.000000 r=186 11 5 22 103 false 4.327731 18569 18650 T A mi1=349 ma1=24.5k mi2=331 ma2=822 pO=0.000000 r=199 22 8 0 108 false 10.000000 18571 18650 T A mi1=359 ma1=24.5k mi2=331 ma2=822 pO=0.000000 r=206 24 3 8 103 false 7.573529 18573 18650 T A mi1=355 ma1=24.4k mi2=331 ma2=822 pO=0.000000 r=208 13 9 5 113 false 8.188406 18574 18650 G A mi1=329 ma1=24.4k mi2=331 ma2=822 pO=0.000000 r=211 9 13 6 102 false 6.000000 18575 18650 A A mi1=384 ma1=24.3k mi2=331 ma2=822 pO=0.000000 r=214 8 2 11 112 false 9.333333 18576 18650 C A mi1=322 ma1=24.1k mi2=331 ma2=822 pO=0.000000 r=217 25 10 4 103 false 6.358025 18577 18650 A A mi1=394 ma1=24.1k mi2=331 ma2=822 pO=0.000000 r=221 11 4 8 114 false 9.661017 18578 18650 G A mi1=329 ma1=23.8k mi2=331 ma2=822 pO=0.000000 r=226 32 10 5 100 false 5.434783 18579 18650 A A mi1=394 ma1=24.0k mi2=331 ma2=822 pO=0.000000 r=232 26 4 10 115 false 7.012195 18581 18650 T A mi1=378 ma1=23.8k mi2=331 ma2=822 pO=0.000000 r=240 13 4 4 110 false 12.222222 18582 18650 C A mi1=326 ma1=24.0k mi2=331 ma2=822 pO=0.000000 r=248 9 6 7 108 false 8.852459 18583 18650 G A mi1=330 ma1=23.8k mi2=331 ma2=822 pO=0.000000 r=258 23 6 3 105 false 8.898305 18585 18650 A A mi1=479 ma1=23.3k mi2=331 ma2=822 pO=0.000000 r=275 37 15 17 117 false 3.545455 18584 18650 T A mi1=1.2k ma1=21.7k mi2=331 ma2=822 pO=0.000000 r=264 24 9 4 118 false 7.763158 18588 18650 T A mi1=727 ma1=19.0k mi2=331 ma2=822 pO=0.000000 r=287 16 12 28 114 false 3.238636 18589 18650 G A mi1=323 ma1=19.3k mi2=331 ma2=822 pO=0.000000 r=292 40 12 5 110 false 5.092593 18590 18650 T A mi1=386 ma1=18.1k mi2=331 ma2=822 pO=0.000000 r=299 15 1 11 116 false 9.206349 18591 18650 C A mi1=308 ma1=17.8k mi2=331 ma2=822 pO=0.000000 r=306 46 4 3 128 false 8.648649 18593 18650 T A mi1=457 ma1=17.3k mi2=331 ma2=822 pO=0.000000 r=314 23 11 24 132 false 4.049080 18594 18650 A A mi1=399 ma1=17.3k mi2=331 ma2=822 pO=0.000000 r=319 41 20 13 128 false 3.699422 18595 18650 T A mi1=509 ma1=16.8k mi2=331 ma2=822 pO=0.000000 r=323 21 8 12 141 false 6.980198 18598 18650 G A mi1=354 ma1=16.0k mi2=331 ma2=822 pO=0.000000 r=347 16 6 21 124 false 5.000000 18599 18650 C A mi1=330 ma1=15.8k mi2=331 ma2=822 pO=0.000000 r=355 28 7 6 124 false 7.750000 18600 18650 A A mi1=413 ma1=15.7k mi2=331 ma2=822 pO=0.000000 r=361 30 3 19 141 false 5.974576 18601 18650 C A mi1=302 ma1=15.6k mi2=331 ma2=822 pO=0.000000 r=365 49 5 2 130 false 8.441558 18602 18650 A A mi1=387 ma1=15.4k mi2=331 ma2=822 pO=0.000000 r=369 18 17 27 141 false 3.634021 18603 18650 T A mi1=373 ma1=15.3k mi2=331 ma2=822 pO=0.000000 r=375 24 17 7 139 false 5.791667 18605 18650 G A mi1=360 ma1=15.0k mi2=331 ma2=822 pO=0.000000 r=393 27 11 27 133 false 3.715084 18606 18650 C A mi1=290 ma1=14.5k mi2=331 ma2=822 pO=0.000000 r=401 38 25 3 128 false 4.266667 18609 18650 T A mi1=413 ma1=14.3k mi2=331 ma2=822 pO=0.000000 r=431 19 21 42 154 false 2.841328 18610 18650 G A mi1=308 ma1=14.4k mi2=331 ma2=822 pO=0.000000 r=440 36 32 6 139 false 3.696809 18611 18

[vtsyvina]

@gianfilippo This is only a part of the file. You need to attach it separately.

Also, variant calling is kinda experimental feature that we added. We never really evaluated it's performance and accuracy. I'd take the results from it with a grain of salt.

[gianfilippo]

Hi, ok but I am a bit lost now. From your paper I understood that the first step is to "extract pairs of statistically linked mutations". Could you please clarify ?

[vtsyvina]

Yes. First step is building the linked graph. We find pairs of SNPs that we suspect should go together in at least one haplotype.

Once this graph is build we go to the next step of finding maximum cliques - sets of SNPs with pair-wise connection. You can see these cliques as small scaffolds since reads cover only limited area of genome(especially Illumina). Now, having these cliques we try to merge them to obtain haplotypes. It's not a trivial step, so I won't go into details.

After we have haplotype candidates the tool splits all reads into clusters(based on the distance to all haplotype candidates) and calculate consensus. In this step some SNPs that we initially identified may go away(whether it was a read error or part of a different haplotype) and some other appear(sometimes we don't have enough statistical evidence for an SNP link, but after reads clustering the SNP appears in consensus). And this is the final answer of the algorithm. This is regular algorithm.

The variant calling part works on top of the algorithm. It takes obtained haplotypes, get all SNPs from them(relative to sample consensus) and tries to estimate frequency. So it is a pretty trivial addition to the main algorithm(we don't discuss it in paper, just added here in repo as experimental feature).

[gianfilippo]

logfile.txt

[gianfilippo]

Hi,

thanks. I reattached the logfile.

Best

[vtsyvina]

It will help if you run without VC, just "-m snv-illumina". This log is only for t=100. SO I cannot compare with what is going on for different choice of t

[antoine4ucsd]

Hello
I am trying to understand this. I tried on the same samples:
option 1: -t default and -tf 0.05
option 2: -t 100 and -tf 0.05
for some samples, I get more haplotypes with option 1 (which I was expecting) but for others, I get more haplotypes with option 2. it is more suprising since I assumed the latter was more stringent?

can you help with that?

[antoine4ucsd]

adding more context, I also tried a third option with t 1000
I got respectively
7 HAP for -t default
8 HAP for -t 100 (more than with t default??)
4 HAP for -t 1000

log files are attached
thank you for your help!

logfile.default.txt
logfile.t100.txt
logfile.t1000.txt