SnpEff: Variant analysis

Contents
Summary
Variant rate by chromosome
Variants by type
Number of variants by impact
Number of variants by functional class
Number of variants by effect
Quality histogram
InDel length histogram
Base variant table
Transition vs transversions (ts/tv)
Allele frequency
Allele Count
Codon change table
Amino acid change table
Chromosome variants plots
Details by gene

Summary

Genome Gallus_gallus-5.0.86
Date 2021-11-16 13:26
SnpEff version
SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
Command line arguments
SnpEff  Gallus_gallus-5.0.86 SRR.vcf.gz -s 
SRR-snpEff_summary.html 
Warnings 10,848
Errors 0
Number of lines (input file) 82,353
Number of variants (before filter) 83,946
Number of not variants
(i.e. reference equals alternative)
0
Number of variants processed
(i.e. after filter and non-variants)
83,283
Number of known variants
(i.e. non-empty ID)
0 ( 0% )
Number of multi-allelic VCF entries
(i.e. more than two alleles)
1,518
Number of effects 212,533
Genome total length 1,230,258,557
Genome effective length 8,220,070
Variant rate 1 variant every 98 bases


Variants rate details

Chromosome Length Variants Variants rate
25 2,906,300 23,967 121
26 5,313,770 59,316 89
Total 8,220,070 83,283 98


Number variants by type

Type Total
SNP 74,300
MNP 0
INS 4,291
DEL 4,692
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 83,283


Number of effects by impact

Type (alphabetical order)   Count Percent
HIGH   142 0.067%
LOW   4,208 1.98%
MODERATE   1,332 0.627%
MODIFIER   206,851 97.327%


Number of effects by functional class

Type (alphabetical order)   Count Percent
MISSENSE   1,285 26.776%
NONSENSE   7 0.146%
SILENT   3,507 73.078%

Missense / Silent ratio: 0.3664


Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
3_prime_UTR_variant   2,484 1.165%
5_prime_UTR_premature_start_codon_gain_variant   75 0.035%
5_prime_UTR_variant   421 0.197%
bidirectional_gene_fusion   18 0.008%
conservative_inframe_deletion   10 0.005%
conservative_inframe_insertion   11 0.005%
disruptive_inframe_deletion   18 0.008%
disruptive_inframe_insertion   17 0.008%
downstream_gene_variant   47,729 22.376%
frameshift_variant   78 0.037%
intergenic_region   35,639 16.708%
intron_variant   71,075 33.321%
missense_variant   1,278 0.599%
non_coding_transcript_exon_variant   1,766 0.828%
non_coding_transcript_variant   1 0%
splice_acceptor_variant   23 0.011%
splice_donor_variant   14 0.007%
splice_region_variant   731 0.343%
start_lost   4 0.002%
stop_gained   10 0.005%
stop_lost   4 0.002%
stop_retained_variant   1 0%
synonymous_variant   3,506 1.644%
upstream_gene_variant   48,390 22.686%

Type (alphabetical order)   Count Percent
DOWNSTREAM   47,729 22.457%
EXON   6,604 3.107%
GENE   18 0.008%
INTERGENIC   35,639 16.769%
INTRON   70,452 33.149%
SPLICE_SITE_ACCEPTOR   21 0.01%
SPLICE_SITE_DONOR   10 0.005%
SPLICE_SITE_REGION   689 0.324%
TRANSCRIPT   1 0%
UPSTREAM   48,390 22.768%
UTR_3_PRIME   2,484 1.169%
UTR_5_PRIME   496 0.233%


Quality:

	
Min30
Max8,507
Mean802.388
Median602
Standard deviation634.329
Values30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,786,787,788,789,790,791,792,793,794,795,796,797,798,799,800,801,802,803,804,805,806,807,808,809,810,811,812,813,814,815,816,817,818,819,820,821,822,823,824,825,826,827,828,829,830,831,832,833,834,835,836,837,838,839,840,841,842,843,844,845,846,847,848,849,850,851,852,853,854,855,856,857,858,859,860,861,862,863,864,865,866,867,868,869,870,871,872,873,874,875,876,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,901,902,903,904,905,906,907,908,909,910,911,912,913,914,915,916,917,918,919,920,921,922,923,924,925,926,927,928,929,930,931,932,933,934,935,936,937,938,939,940,941,942,943,944,945,946,947,948,949,950,951,952,953,954,955,956,957,958,959,960,961,962,963,964,965,966,967,968,969,970,971,972,973,974,975,976,977,978,979,980,981,982,983,984,985,986,987,988,989,990,991,992,993,994,995,996,997,998,999,1000,1001,1002,1003,1004,1005,1006,1007,1008,1009,1010,1011,1012,1013,1014,1015,1016,1017,1018,1019,1020,1021,1022,1023,1024,1025,1026,1027,1028,1029,1030,1031,1032,1033,1034,1035,1036,1037,1038,1039,1040,1041,1042,1043,1044,1045,1046,1047,1048,1049,1050,1051,1052,1053,1054,1055,1056,1057,1058,1059,1060,1061,1062,1063,1064,1065,1066,1067,1068,1069,1070,1071,1072,1073,1074,1075,1076,1077,1078,1079,1080,1081,1082,1083,1084,1085,1086,1087,1088,1089,1090,1091,1092,1093,1094,1095,1096,1097,1098,1099,1100,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1111,1112,1113,1114,1115,1116,1117,1118,1119,1120,1121,1122,1123,1124,1125,1126,1127,1128,1129,1130,1131,1132,1133,1134,1135,1136,1137,1138,1139,1140,1141,1142,1143,1144,1145,1146,1147,1148,1149,1150,1151,1152,1153,1154,1155,1156,1157,1158,1159,1160,1161,1162,1163,1164,1165,1166,1167,1168,1169,1170,1171,1172,1173,1174,1175,1176,1177,1178,1179,1180,1181,1182,1183,1184,1185,1186,1187,1188,1189,1190,1191,1192,1193,1194,1195,1196,1197,1198,1199,1200,1201,1202,1203,1204,1205,1206,1207,1208,1209,1210,1211,1212,1213,1214,1215,1216,1217,1218,1219,1220,1221,1222,1223,1224,1225,1226,1227,1228,1229,1230,1231,1232,1233,1234,1235,1236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Count32,22,33,29,44,37,71,16,29,27,27,25,41,33,34,34,48,36,47,46,53,39,28,50,50,40,50,43,46,40,69,48,46,62,52,38,39,42,50,65,50,54,49,38,42,27,24,102,66,151,33,44,29,44,52,36,37,53,48,41,49,50,44,59,52,29,48,38,46,64,46,56,64,42,43,67,48,46,59,58,44,73,49,54,60,46,46,46,43,48,82,74,126,45,50,46,66,47,48,63,43,41,54,59,68,70,41,51,71,56,62,81,59,51,70,68,57,84,64,61,67,56,56,73,59,64,87,70,78,70,57,51,68,52,79,67,57,108,86,83,67,86,84,62,73,51,69,66,51,60,84,65,68,91,72,56,76,86,77,71,56,65,95,80,77,91,81,64,90,74,81,87,75,77,82,81,71,65,66,129,96,65,99,108,69,81,82,66,81,88,90,89,99,75,89,104,80,62,103,85,86,90,73,91,87,67,78,74,79,103,86,72,76,101,89,93,106,80,87,100,69,72,103,81,91,130,83,102,115,95,74,128,74,77,118,79,77,105,84,82,102,85,76,94,98,66,105,83,98,87,94,95,104,90,96,90,88,73,115,82,96,123,75,93,87,88,75,115,112,116,126,99,114,126,82,73,113,95,100,91,56,92,85,92,76,98,105,89,83,79,81,106,79,82,118,89,91,100,88,89,133,86,96,114,89,89,127,87,80,124,75,79,112,99,112,94,95,102,107,96,68,91,75,82,86,71,99,89,74,71,96,81,87,89,73,86,122,65,88,96,74,82,105,77,82,104,66,98,108,72,88,108,76,69,105,63,64,105,78,100,91,73,83,89,76,84,87,87,77,103,70,77,102,73,82,105,89,69,92,69,80,102,60,72,90,85,69,105,90,70,116,68,70,99,74,75,94,69,79,85,51,58,103,67,99,77,87,74,81,69,69,82,59,70,80,81,68,103,79,69,71,54,69,94,65,64,90,75,79,106,70,85,67,84,70,106,78,67,76,48,71,80,61,58,74,76,50,80,59,105,70,75,84,81,48,56,76,64,53,73,46,61,67,72,51,88,51,51,113,62,61,85,54,63,77,60,52,74,61,40,70,62,59,84,54,65,54,62,55,85,56,62,74,56,97,76,46,67,78,67,69,78,45,61,64,49,66,70,49,48,77,43,56,61,44,49,71,52,47,73,33,53,59,61,45,61,53,43,56,60,46,66,59,57,51,63,55,58,67,73,69,61,66,59,56,53,63,56,58,57,61,55,71,46,46,53,41,40,44,42,43,69,54,55,51,51,32,70,52,53,67,40,45,56,60,55,56,54,50,49,45,58,66,52,95,51,42,43,46,37,61,67,39,47,61,38,42,56,46,45,55,54,50,50,37,41,50,37,38,49,44,43,54,42,36,50,44,45,48,48,52,61,40,50,48,43,37,37,46,85,49,50,38,45,39,32,33,50,46,44,29,45,46,33,47,59,39,35,63,35,50,32,46,47,45,57,54,33,29,56,32,40,35,45,45,37,39,44,58,32,34,51,46,37,86,53,41,38,37,39,34,44,37,40,43,35,36,35,27,43,50,47,35,48,34,43,39,49,47,48,29,46,49,26,52,34,35,45,53,50,40,31,34,38,45,38,49,44,47,95,39,35,44,37,44,37,34,37,34,32,36,34,27,27,31,41,36,34,45,38,37,36,39,45,39,33,38,39,29,41,32,46,47,36,46,39,35,36,35,39,23,28,48,31,71,35,51,39,37,36,39,40,36,41,40,33,44,39,41,34,33,41,47,34,36,39,33,37,35,39,44,37,34,29,44,44,57,42,49,41,52,41,33,35,35,32,31,43,32,93,29,30,32,40,30,41,41,41,25,44,32,29,26,31,35,35,39,48,26,36,40,38,34,45,37,30,47,38,30,49,35,47,36,45,40,51,26,46,24,33,37,48,31,36,92,30,42,25,33,40,31,46,33,37,32,37,25,34,37,31,24,36,38,36,35,30,44,29,44,40,45,38,41,27,29,42,39,40,59,36,34,40,34,30,35,29,32,27,43,84,42,36,34,24,35,30,26,25,38,39,35,35,33,26,21,38,22,34,26,34,21,37,30,33,36,39,42,38,36,38,38,40,39,34,41,42,38,40,39,20,38,36,34,37,74,30,36,27,24,36,36,37,40,34,28,37,30,31,34,33,43,31,17,32,24,33,34,35,35,46,26,31,30,32,31,25,35,37,40,28,40,34,31,42,37,29,22,24,36,89,34,28,30,26,29,29,37,36,30,39,37,26,29,25,29,23,32,28,28,34,25,23,31,35,27,37,30,32,43,33,28,25,36,30,33,35,41,33,23,25,32,20,33,29,81,38,36,42,33,25,31,28,33,31,33,32,22,20,18,36,26,16,26,21,28,26,31,38,25,37,29,35,38,46,30,34,34,38,29,37,20,26,19,29,30,17,38,29,32,75,24,19,36,19,31,26,31,23,26,23,28,28,25,21,32,20,35,38,25,36,24,19,36,42,24,32,18,34,24,30,40,24,37,36,37,31,28,30,34,21,21,22,23,34,76,30,24,25,25,27,22,28,24,27,36,23,23,24,32,28,21,25,35,19,24,25,27,30,26,15,23,30,29,35,29,34,41,23,30,35,26,40,40,22,31,29,28,26,24,62,34,21,23,27,26,29,24,22,35,24,21,26,22,33,21,21,22,22,19,25,28,36,27,18,26,25,25,21,34,36,19,35,26,24,39,31,37,23,23,17,26,25,26,31,67,20,26,24,22,16,23,13,23,20,20,25,24,22,39,22,29,22,28,24,26,19,25,29,25,20,34,26,38,25,18,32,33,24,17,32,24,21,23,24,29,27,37,18,41,62,21,22,24,17,22,24,14,23,18,24,13,29,24,19,16,25,26,26,21,27,25,28,32,19,17,30,22,19,32,29,30,24,26,28,32,25,20,28,27,20,15,25,16,19,49,20,24,20,25,29,17,18,25,23,22,27,28,15,24,16,22,23,27,28,24,27,23,21,20,22,26,20,22,31,18,25,17,25,39,30,26,22,18,20,24,25,15,20,26,60,16,24,23,21,15,18,28,18,11,9,19,11,16,18,23,23,18,26,28,27,22,19,20,31,25,22,18,18,32,28,29,19,24,24,27,27,18,26,27,27,19,16,13,26,53,20,19,23,25,10,18,19,17,18,26,24,19,21,18,21,29,23,25,27,20,19,38,30,11,21,21,18,18,18,23,20,21,24,16,17,16,18,19,23,20,34,14,21,29,48,17,24,16,21,29,15,18,27,20,16,25,20,17,16,29,21,16,19,19,24,18,20,21,25,14,14,15,17,17,16,16,21,17,21,22,18,14,22,20,10,18,24,24,16,46,24,17,25,20,21,21,23,22,15,21,23,14,13,22,20,12,16,15,26,26,26,19,18,16,24,21,16,21,21,14,19,22,17,21,32,26,8,19,22,15,12,15,16,16,38,19,17,29,11,17,17,18,20,20,12,19,25,22,19,20,8,19,17,16,27,20,16,17,26,15,19,16,23,20,17,19,17,14,16,26,22,15,23,27,12,16,21,15,20,36,17,17,12,10,13,14,9,18,15,16,20,21,13,13,15,18,21,19,19,16,14,14,18,14,14,14,11,16,18,13,10,15,13,26,17,17,14,20,13,8,7,24,8,14,35,21,15,12,18,10,8,24,12,17,16,13,33,20,14,15,12,8,14,18,14,17,9,15,12,9,12,15,9,15,21,17,21,19,29,19,8,6,13,17,8,12,17,18,14,29,17,11,12,20,15,15,13,21,9,22,11,16,19,15,20,13,11,15,13,19,13,11,18,20,15,11,17,14,18,16,10,25,12,23,19,25,18,18,14,20,13,10,16,17,27,13,12,11,9,9,11,14,14,14,12,16,10,13,12,8,16,12,10,12,15,11,22,21,14,8,19,13,8,8,9,8,10,12,14,15,9,18,15,14,17,11,15,17,12,29,9,8,13,14,16,11,12,8,15,13,13,13,15,17,12,10,16,12,14,17,16,12,13,15,10,8,10,16,12,21,20,12,8,12,9,16,14,15,14,10,11,15,10,15,32,12,12,13,7,11,12,13,9,7,13,13,14,8,3,6,11,16,12,15,14,12,16,13,18,19,15,15,20,13,15,20,15,17,7,18,13,18,8,12,10,8,15,11,9,20,7,8,18,6,19,10,15,17,7,4,8,7,9,14,14,11,12,12,9,10,13,11,16,8,13,18,11,7,13,11,9,16,9,17,14,11,7,8,11,10,14,13,9,12,16,7,8,7,13,7,12,12,14,8,8,14,10,10,18,10,10,11,12,13,8,7,12,8,19,11,7,7,12,12,13,7,17,21,6,8,7,10,6,6,5,14,8,6,10,23,14,9,12,10,8,8,5,12,12,11,11,9,18,13,6,9,10,6,10,5,8,15,14,12,16,10,8,13,8,4,10,12,10,11,18,10,13,10,7,6,11,5,7,10,20,15,11,8,8,13,12,12,7,9,7,19,4,7,9,12,10,9,5,10,13,5,13,9,11,11,8,9,9,8,7,8,9,10,9,9,10,11,8,6,8,9,3,8,5,19,7,2,8,10,11,2,8,7,8,9,8,13,7,8,9,5,7,7,5,11,13,9,8,9,4,11,10,2,4,12,11,11,10,7,11,7,8,8,7,12,6,10,6,12,20,8,5,10,10,7,7,8,10,7,11,10,7,7,8,10,3,3,8,5,6,12,8,9,7,11,11,4,7,11,6,4,5,14,7,12,7,14,6,9,5,7,9,7,9,22,7,11,5,2,6,3,6,6,9,7,7,12,4,6,7,13,7,11,7,5,12,7,5,2,7,9,10,3,3,3,6,5,7,13,5,8,8,7,6,12,7,6,7,6,9,1,9,7,11,6,4,2,3,4,2,5,8,7,8,11,10,9,4,7,5,11,10,5,7,9,11,4,6,7,4,7,5,6,10,3,9,12,4,13,9,2,6,4,23,8,4,7,7,8,5,4,8,3,4,6,15,9,5,5,10,5,4,7,11,7,8,9,4,4,9,6,5,6,5,8,9,4,7,6,7,5,4,3,6,4,5,8,11,4,5,5,5,2,6,4,3,2,6,4,8,11,5,2,11,7,9,10,6,6,9,2,5,9,5,5,4,6,6,1,6,2,5,6,5,5,3,5,5,2,3,7,14,6,5,5,7,6,4,7,5,7,8,8,4,5,1,4,3,3,9,9,6,5,4,4,5,4,7,3,5,5,1,4,5,4,4,8,6,5,2,5,5,4,2,5,18,2,5,6,6,8,4,5,4,5,6,1,5,6,5,5,2,4,3,3,6,5,5,4,9,4,5,6,5,3,3,2,8,5,2,5,3,3,6,5,4,3,4,2,10,2,3,4,2,4,5,5,2,6,3,7,3,3,4,11,6,4,6,1,3,8,4,4,2,5,4,2,1,6,3,2,4,2,7,3,5,2,2,4,5,4,2,3,12,3,5,2,1,6,4,2,3,4,4,1,2,3,4,4,2,2,5,5,3,2,3,9,7,4,4,2,2,5,5,4,2,1,2,6,6,3,1,1,5,7,4,4,17,4,3,2,4,2,5,2,3,4,1,1,3,4,5,1,2,4,2,4,9,1,4,3,2,4,4,5,1,4,1,8,6,5,3,2,3,8,5,4,6,3,2,22,1,2,6,2,2,5,1,3,3,2,5,2,6,3,4,5,2,4,1,2,6,4,2,4,3,2,3,2,3,2,5,4,1,4,2,3,1,3,5,1,5,7,1,7,1,1,1,4,1,3,4,2,7,3,2,7,3,2,1,2,3,3,3,2,1,5,1,1,1,4,1,11,3,3,2,5,8,6,2,1,7,2,5,2,9,2,3,3,1,2,4,5,3,2,1,3,3,2,3,7,1,2,6,3,1,2,3,5,2,1,4,2,4,4,3,2,2,1,2,2,3,3,8,2,2,5,3,1,2,3,3,4,1,1,3,3,1,1,1,4,4,3,4,1,2,1,5,2,3,4,1,2,6,1,2,6,2,10,1,3,1,1,2,4,2,3,1,6,1,3,2,3,8,3,3,2,3,3,2,3,1,2,3,1,3,1,1,2,4,1,2,2,2,2,6,1,1,2,2,2,3,1,1,1,1,4,1,3,4,4,1,1,1,2,2,2,2,1,2,3,1,2,1,4,4,1,5,8,3,1,2,3,2,10,1,2,1,2,2,2,3,2,1,1,3,2,2,2,2,3,4,1,1,5,1,2,2,1,1,3,3,3,1,1,3,1,1,1,4,1,1,3,1,5,1,2,1,1,6,1,1,2,1,3,3,1,2,2,1,2,3,3,2,1,5,2,1,4,1,1,1,6,3,1,1,3,1,1,2,1,3,1,2,1,1,1,1,1,2,3,1,1,3,2,1,2,3,2,3,2,1,3,1,1,2,1,2,2,1,2,1,1,2,2,5,1,1,3,2,2,4,2,1,2,2,3,1,2,2,2,2,2,1,1,3,5,1,4,1,1,1,1,3,1,1,2,1,3,4,3,1,2,1,1,3,2,1,1,4,2,2,1,1,1,1,3,1,1,2,1,1,2,1,1,1,2,1,1,1,2,2,1,1,1,1,1,2,1,2,2,1,1,1,1,2,1,2,2,2,2,2,2,2,1,2,1,6,1,1,1,1,1,1,1,1,1,1,2,1,2,1,1,1,1,1,2,2,2,1,1,1,1,2,1,2,1,1,2,1,1,2,1,2,1,1,1,1,2,1,1,1,1,1,1,3,3,1,1,1,1,1,1,1,2,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,2,1,2,1,1,1,2,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,2,1,2,1,1,1,2,1,1,2,1,1,1,1,1,1,1,1,1,1,1,5,2,1,1,1,2,1,2,1,1,2,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,2


Insertions and deletions length:

	
Min0
Max249
Mean2.275
Median1
Standard deviation7.284
Values0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,44,45,46,47,49,50,52,55,56,57,59,62,65,67,68,70,89,90,92,95,106,109,122,173,223,249
Count1903,5483,394,221,156,115,84,85,73,66,31,38,29,23,29,22,16,23,10,21,14,7,11,12,4,4,6,2,8,4,3,9,3,1,3,3,2,3,3,3,3,4,9,1,1,2,3,3,2,2,1,2,1,1,3,1,2,1,3,1,1,2,1,1,2,1,1,1


Base changes (SNPs)

  A C G T
A 0 2,243 12,249 2,042
C 2,574 0 2,806 15,210
G 14,976 2,799 0 2,538
T 1,964 12,656 2,243 0


Ts/Tv (transitions / transversions)

Note: Only SNPs are used for this statistic.
Note: This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).

Transitions 114,879
Transversions 39,402
Ts/Tv ratio 2.9156

All variants:

Sample ,SRR7062654,SRR7062655,Total
Transitions ,58351,56528,114879
Transversions ,20081,19321,39402
Ts/Tv ,2,906,2,926,2,916

Only known variants (i.e. the ones having a non-empty ID field):

No results available (empty input?)


Allele frequency


Min25
Max100
Mean53.819
Median50
Standard deviation28.319
Values25,50,75,100
Count31704,22168,12678,15803


Allele Count


Min1
Max4
Mean2.119
Median2
Standard deviation1.115
Values1,2,3,4
Count32228,22792,12678,14655


Hom/Het per sample




Sample_names , SRR7062654, SRR7062655
Reference , 24290, 19698
Het , 26055, 37571
Hom , 31308, 24112
Missing , 700, 972


Codon changes

How to read this table:
- Rows are reference codons and columns are changed codons. E.g. Row 'AAA' column 'TAA' indicates how many 'AAA' codons have been replaced by 'TAA' codons.
- Red background colors indicate that more changes happened (heat-map).
- Diagonals are indicated using grey background color
- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).

  - AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT
-   2   6 1 2 17   5 3 3 9 2   5   1 4 6 12 11 6 13 1 1   1 1 2 3 7 2 6 2   8 6 6 1   3 12 10 8 4   4 6     5   1 4 13 7   3 13   13   3   3
AAA 1     51 1 2       8               1                               2                                                              
AAC   1     96   1       14               1                               8                                                            
AAG 7 25 5   1     4       10                                               9                                                          
AAT     59           1       1                                               5                                                        
ACA 1 6   1     10 76 10 1       5   1           1                               15                               2                      
ACC 12   2     7 4 8 42   10       2                                               18                               3                    
ACG 2     2   124 4   3             23                                               1                               3                  
ACT 2         5 43 3         1       3                                               11                               1                
AGA   9       1       1   22                           5                               1                                              
AGC 2   15       3     3 1   80                           1                               16                               1            
AGG       14       1   16 4                                 4                               5                                          
AGT 3       2     1 1 2 56 1         1                       4                               1                                        
ATA           2       1         2 1 3                                                         4                                      
ATC 4   1       3             6   2 73                           2                               21                                    
ATG 1             14       3   7     7                             3                               13                               2  
ATT 2               2         2 50 2                                 2                               8           2                    
CAA 1                                   2 29 1 1       1               2                                                              
CAC 3   1                             1   4 80           13       3                                       4                            
CAG 10     10                           45 3 1 1 2           6       4       1                                                          
CAT 6                                   42 4         1       11       1       4                               1                        
CCA 8         4                                 15 92 3 1       5                                               2                      
CCC 11                                   1     10   13 90           15               5                               9                    
CCG 1                                     3   99 11   14             16               1                               4                  
CCT 2               1                         9 70 8         2       2                                               14                
CGA 1                 6               12       1         8 13 9                         1                               2              
CGC 1                   2               13       4 1       5 35                           1                               9            
CGG                       7               26           15 6   4                                                             12          
CGT 1                                       16       2 2 33 1         2                       2                               2        
CTA 1                                         5                 1 23 1                                                         4      
CTC 4                           4               6             1   30 44                           1                               3    
CTG 2                             2       2       19           24 20   7                             2                               57  
CTT 1                                               1       1   26 10                                                                 3
GAA 3 6               1               3                                 6 53   4       1       2                                      
GAC 2   10                                                               1 6 83   2       2       2                                    
GAG 12     9                               3                           81 8 2 2     3       5       2                                  
GAT 5       7                                                         1 78 2         1       2               1                        
GCA 4         15                               2                       1         9 50 9 2       10                                      
GCC 2           13                               5 1     1                     9   7 84   2       18               5                    
GCG               8                               2                       6   103 2   3   1 3       20                                  
GCT 1               15                               1                         7 58 2         1       7               2                
GGA 1                 4                               4               3                 7 16 7                                        
GGC 4                   23                                               11       6     12   20 43                           1            
GGG 8                     11                               3               8 1     3   23 23   6     4                       4          
GGT 5                       10                               1               2       3 7 30 4         1                     1 1        
GTA                           6                               1               1       4         2 13 1                                
GTC 2                           31                               1       2       8       2     1   22 30                                
GTG 7                             23                               8       5       16       1 1 18 13   11                             2  
GTT                                 7                               4               14           15 8                                  
TAA                                                                                                                   1              
TAC 1   1                               2                                                                   79   3       4       3    
TAG                                       2                                                                                          
TAT 4                                       5                                                         1 52 1         1       1       4
TCA 1                                         2                                                                 6 57 3         2      
TCC 4                                           10                               1                       2     7   3 64   1       3    
TCG               1                               2                                                           63 5   7             7  
TCT 1               4                               5                               4                       1 8 59 2         1       1
TGA                                                   1                               1                                              
TGC 6                                                   5                                               1                 1 46        
TGG 1                                                     5                                                       1   3 1   1        
TGT 2                                                       3                               1               2       1   50 1          
TTA                           1                               7                               2               1                 1 10  
TTC 2                           1                               10                               1       3       1       2         4 52
TTG 2                             3                               41                               1               2       5   3   3 4
TTT 5                               1                               5                                       5       2         1 36 2  


Amino acid changes

How to read this table:
- Rows are reference amino acids and columns are changed amino acids. E.g. Row 'A' column 'E' indicates how many 'A' amino acids have been replaced by 'E' amino acids.
- Red background colors indicate that more changes happened (heat-map).
- Diagonals are indicated using grey background color
- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).

  * - ? A C D E F G H I K L M N P Q R S T V W Y
* 1               1               2 1          
- 3   41 10 26 6 10 6 34 17 6 8 18   1 21 16 16 29 24 10   6
?                                              
A   7   343     7   9             11   1 7 51 55    
C   8     96       1                 8 1     2 3
D   7   3   162 9   4           17           2   1
E   15   7   16 136   6     15         6 1     4    
F   7     2     88     2   22           3   1   8
G   18   12 2 14 11   198                 23 33   5 5  
H   9       4       122     4   1 1 9 24         5
I   6                 136   4 5 1     1 2 7 33    
K   8         11         76     7   1 18   6      
L   10           11     5   312 5   31 2 1 3   6 5  
M   1                 14   5         3   14 13    
N           13       1   1     155       15 2      
P   22   6           1     38     434 3 3 29 5      
Q   11         3     7   10 4     3 75 7          
R 2 3     11       10 29   23 2     8 38 192 6 2   12  
S   11   5 3     4 17   1   9   17 19   11 421 10     3
T   17   45             10 9   24 2 1   1 20 339      
V   9   39   2 5   8   44   16 23             134    
W 3 1     2                         5 1        
Y 2 5     5     7   7         1       4       131


Variants by chromosome

		
25, Position,0,10000,20000,30000,40000,50000,60000,70000,80000,90000,100000,110000,120000,130000,140000,150000,160000,170000,180000,190000,200000,210000,220000,230000,240000,250000,260000,270000,280000,290000,300000,310000,320000,330000,340000,350000,360000,370000,380000,390000,400000,410000,420000,430000,440000,450000,460000,470000,480000,490000,500000,510000,520000,530000,540000,550000,560000,570000,580000,590000,600000,610000,620000,630000,640000,650000,660000,670000,680000,690000,700000,710000,720000,730000,740000,750000,760000,770000,780000,790000,800000,810000,820000,830000,840000,850000,860000,870000,880000,890000,900000,910000,920000,930000,940000,950000,960000,970000,980000,990000,1000000,1010000,1020000,1030000,1040000,1050000,1060000,1070000,1080000,1090000,1100000,1110000,1120000,1130000,1140000,1150000,1160000,1170000,1180000,1190000,1200000,1210000,1220000,1230000,1240000,1250000,1260000,1270000,1280000,1290000,1300000,1310000,1320000,1330000,1340000,1350000,1360000,1370000,1380000,1390000,1400000,1410000,1420000,1430000,1440000,1450000,1460000,1470000,1480000,1490000,1500000,1510000,1520000,1530000,1540000,1550000,1560000,1570000,1580000,1590000,1600000,1610000,1620000,1630000,1640000,1650000,1660000,1670000,1680000,1690000,1700000,1710000,1720000,1730000,1740000,1750000,1760000,1770000,1780000,1790000,1800000,1810000,1820000,1830000,1840000,1850000,1860000,1870000,1880000,1890000,1900000,1910000,1920000,1930000,1940000,1950000,1960000,1970000,1980000,1990000,2000000,2010000,2020000,2030000,2040000,2050000,2060000,2070000,2080000,2090000,2100000,2110000,2120000,2130000,2140000,2150000,2160000,2170000,2180000,2190000,2200000,2210000,2220000,2230000,2240000,2250000,2260000,2270000,2280000,2290000,2300000,2310000,2320000,2330000,2340000,2350000,2360000,2370000,2380000,2390000,2400000,2410000,2420000,2430000,2440000,2450000,2460000,2470000,2480000,2490000,2500000,2510000,2520000,2530000,2540000,2550000,2560000,2570000,2580000,2590000,2600000,2610000,2620000,2630000,2640000,2650000,2660000,2670000,2680000,2690000,2700000,2710000,2720000,2730000,2740000,2750000,2760000,2770000,2780000,2790000,2800000,2810000,2820000,2830000,2840000,2850000,2860000,2870000,2880000,2890000,2900000 25,Count,153,185,122,170,16,63,89,101,68,160,94,89,124,102,123,130,93,75,90,47,61,125,78,104,82,142,184,140,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,48,72,143,91,92,8,85,48,38,220,110,171,95,107,100,144,85,54,83,106,161,156,143,150,269,178,331,109,87,78,85,73,70,63,62,71,111,118,157,61,4,53,110,152,123,88,150,123,129,114,121,140,147,116,115,52,77,68,93,73,144,125,107,99,70,82,127,91,130,130,109,66,61,70,84,122,108,110,85,75,97,103,3,66,70,73,25,10,73,95,126,36,63,79,115,84,103,105,87,160,90,111,64,32,73,88,67,120,86,174,138,149,158,123,104,152,136,92,146,114,137,130,145,165,145,118,178,148,70,21,110,96,58,71,70,148,63,142,45,156,109,98,116,108,130,72,101,129,180,167,117,114,145,145,140,68,149,123,119,128,155,129,169,152,159,148,96,151,134,178,104,142,142,123,93,150,117,156,33,67,52,102,58,102,40,6,1,1,30,28,3,4,21,102,74,98,94,128,62,50,28,14,86,30,6,20,26,43,22,21,25,23,19
		
26, Position,0,100000,200000,300000,400000,500000,600000,700000,800000,900000,1000000,1100000,1200000,1300000,1400000,1500000,1600000,1700000,1800000,1900000,2000000,2100000,2200000,2300000,2400000,2500000,2600000,2700000,2800000,2900000,3000000,3100000,3200000,3300000,3400000,3500000,3600000,3700000,3800000,3900000,4000000,4100000,4200000,4300000,4400000,4500000,4600000,4700000,4800000,4900000,5000000,5100000,5200000,5300000 26,Count,281,146,294,1112,1246,1356,1117,1167,1126,1238,1135,1041,811,1400,1677,1459,1220,1185,1566,1375,1224,1311,1292,1491,1293,1393,1384,1656,1309,1100,1515,1055,1115,1115,1401,937,1087,1058,1238,1258,1055,852,994,1122,1446,1170,941,892,1236,1002,750,314,313,45

Details by gene

Here you can find a tab-separated table.