SnpEff: Variant analysis
Genome | chm13 |
Date | 2020-10-07 11:19 |
SnpEff version | SnpEff 5.0 (build 2020-08-09 21:23), by Pablo Cingolani |
Command line arguments | SnpEff chm13 ../all.vcf |
Warnings | 0 |
Errors | 0 |
Number of lines (input file) | 191,759 |
Number of variants (before filter) | 192,697 |
Number of not variants (i.e. reference equals alternative) |
0 |
Number of variants processed (i.e. after filter and non-variants) |
144,424 |
Number of known variants (i.e. non-empty ID) |
0 ( 0% ) |
Number of multi-allelic VCF entries (i.e. more than two alleles) |
921 |
Number of effects | 144,424 |
Genome total length | 3,114,143,937 |
Genome effective length | 51,353,906 |
Variant rate | 1 variant every 355 bases |
Chromosome | Length | Variants | Variants rate |
---|---|---|---|
22 | 51,353,906 | 144,424 | 355 |
Total | 51,353,906 | 144,424 | 355 |
Type | Total |
---|---|
SNP | 144,292 |
MNP | 0 |
INS | 84 |
DEL | 48 |
MIXED | 0 |
INV | 0 |
DUP | 0 |
BND | 0 |
INTERVAL | 0 |
Total | 144,424 |
Type (alphabetical order) | Count | Percent | |
---|---|---|---|
MODIFIER | 144,424 | 100% |
Type (alphabetical order) | Count | Percent |
---|
Missense / Silent ratio: 0
Type | Region | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
Quality:
Min | 3 |
---|---|
Max | 150 |
Mean | 139.724 |
Median | 150 |
Standard deviation | 24.672 |
Values | 3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,29,30,39,48,50,58,69,80,82,90,140,150 |
Count | 15,2,30,36,2,1,9,11,1,5,15,1,4,5,5,9,3,20,6,3,12,19,24,10,1230,2,15,1,1,1,16757,1,8749,8944,155810 |
Insertions and deletions length:
Min | 0 |
---|---|
Max | 271 |
Mean | 8.856 |
Median | 1 |
Standard deviation | 32.008 |
Values | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,15,20,27,30,58,176,271 |
Count | 31,54,3,3,1,2,1,1,2,7,4,7,4,2,3,1,1,1,1,2,1 |
A | C | G | T | |
---|---|---|---|---|
A | 0 | 12,591 | 12,054 | 13,530 |
C | 12,473 | 0 | 11,014 | 11,806 |
G | 11,701 | 11,032 | 0 | 11,465 |
T | 13,280 | 11,760 | 11,586 | 0 |
Note: This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).
Transitions | 2,657,023 |
---|---|
Transversions | 5,452,615 |
Ts/Tv ratio | 0.4873 |
All variants:
Sample ,alignment/HG00514.bam,alignment/HG00733.bam,alignment/HG00735.bam,alignment/HG00741.bam,alignment/HG01071.bam,alignment/HG01106.bam,alignment/HG01123.bam,alignment/HG01175.bam,alignment/HG01358.bam,alignment/HG01361.bam,alignment/HG01891.bam,alignment/HG01928.bam,alignment/HG01952.bam,alignment/HG01978.bam,alignment/HG02148.bam,alignment/HG02257.bam,alignment/HG02486.bam,alignment/HG02559.bam,alignment/HG02572.bam,alignment/HG02622.bam,alignment/HG02630.bam,alignment/HG02717.bam,alignment/HG02723.bam,alignment/HG02818.bam,alignment/HG02886.bam,alignment/HG02970.bam,alignment/HG03125.bam,alignment/HG03453.bam,alignment/HG03471.bam,alignment/HG03516.bam,alignment/HG03540.bam,alignment/HG03579.bam,alignment/NA12878.bam,alignment/NA18906.bam,alignment/NA19030.bam,alignment/NA19238.bam,alignment/NA19239.bam,alignment/NA19240.bam,alignment/NA20300.bam,Total Transitions ,76288,69938,82293,87167,90432,84683,74911,81424,77954,78554,76606,85005,86836,85779,80245,78698,80888,78842,78301,84339,82004,81167,80121,75677,78253,113,79096,81715,79,82710,82988,83468,68206,89888,119,123,102,71866,145,2657023 Transversions ,156480,143402,168877,179420,185920,174069,153834,167103,160087,161180,157168,174589,177944,176004,164864,161493,166029,161479,160783,173396,168439,166724,164308,155175,160426,42,162228,167775,34,169755,170310,171370,139884,184366,40,46,40,147466,66,5452615 Ts/Tv ,0.488,0.488,0.487,0.486,0.486,0.486,0.487,0.487,0.487,0.487,0.487,0.487,0.488,0.487,0.487,0.487,0.487,0.488,0.487,0.486,0.487,0.487,0.488,0.488,0.488,2.690,0.488,0.487,2.324,0.487,0.487,0.487,0.488,0.488,2.975,2.674,2.550,0.487,2.197,0.487
Only known variants (i.e. the ones having a non-empty ID field):
No results available (empty input?)
Min | 1 |
---|---|
Max | 100 |
Mean | 72.398 |
Median | 84 |
Standard deviation | 24.858 |
Values | 1,2,3,5,6,7,8,10,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,28,29,30,31,32,33,34,35,37,38,39,40,41,42,43,44,45,46,47,48,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,96,97,98,100 |
Count | 200,4825,38,2632,30,2107,14,647,16,1014,15,7,2034,2,1144,16,5,752,8,387,3,1187,9,225,6,410,2,4,464,11,359,3,58,15,1,510,13,569,16,1,702,4,178,33,1286,21,691,3,26,1044,5,313,1,6,317,8,4,257,9,639,16,13,1329,4,565,4,27,3423,13,2670,28,2749,18,39,2699,135,104024,170,40,30,36,18,25,46,14,15,7,10,7,6 |
Min | 1 |
---|---|
Max | 78 |
Mean | 56.909 |
Median | 66 |
Standard deviation | 19.421 |
Values | 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78 |
Count | 200,4826,37,2636,26,2108,13,647,16,1030,7,2035,2,1163,5,755,5,387,3,1191,5,226,5,412,4,470,5,361,2,71,4,519,5,581,4,709,1,204,6,1300,8,711,5,1049,1,328,1,323,7,265,4,678,15,1343,2,570,12,3433,12,2670,21,2831,18,2833,54,103937,170,30,32,13,25,46,13,13,7,8,7,5 |
Sample_names , alignment/HG00514.bam, alignment/HG00733.bam, alignment/HG00735.bam, alignment/HG00741.bam, alignment/HG01071.bam, alignment/HG01106.bam, alignment/HG01123.bam, alignment/HG01175.bam, alignment/HG01358.bam, alignment/HG01361.bam, alignment/HG01891.bam, alignment/HG01928.bam, alignment/HG01952.bam, alignment/HG01978.bam, alignment/HG02148.bam, alignment/HG02257.bam, alignment/HG02486.bam, alignment/HG02559.bam, alignment/HG02572.bam, alignment/HG02622.bam, alignment/HG02630.bam, alignment/HG02717.bam, alignment/HG02723.bam, alignment/HG02818.bam, alignment/HG02886.bam, alignment/HG02970.bam, alignment/HG03125.bam, alignment/HG03453.bam, alignment/HG03471.bam, alignment/HG03516.bam, alignment/HG03540.bam, alignment/HG03579.bam, alignment/NA12878.bam, alignment/NA18906.bam, alignment/NA19030.bam, alignment/NA19238.bam, alignment/NA19239.bam, alignment/NA19240.bam, alignment/NA20300.bam Reference , 26234, 36031, 16949, 9241, 4331, 13151, 28294, 18315, 23585, 22790, 25751, 12737, 10082, 11631, 20027, 22512, 19113, 22445, 23068, 13692, 17341, 18624, 20361, 27222, 23258, 143167, 21925, 17814, 143261, 16341, 15865, 15129, 38703, 5380, 143143, 143152, 143168, 33027, 143150 Het , 106, 0, 101, 105, 135, 133, 81, 19, 9, 0, 0, 24, 0, 23, 96, 83, 98, 115, 62, 84, 111, 51, 71, 104, 94, 233, 110, 125, 203, 57, 0, 114, 0, 102, 246, 210, 258, 108, 96 Hom , 117109, 107366, 126393, 134124, 139003, 130181, 115103, 125089, 119824, 120688, 117667, 130658, 133277, 131761, 123339, 120876, 124260, 120914, 120327, 129694, 126024, 124773, 123025, 116137, 120102, 70, 121435, 125537, 17, 127066, 127509, 128225, 104726, 137977, 70, 91, 41, 110338, 207 Missing , 37, 89, 43, 16, 17, 21, 8, 63, 68, 8, 68, 67, 127, 71, 24, 15, 15, 12, 29, 16, 10, 38, 29, 23, 32, 16, 16, 10, 5, 22, 112, 18, 57, 27, 27, 33, 19, 13, 33
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).
- 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).
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).
- 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).
22, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000 22,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,144424,0,0,0,0,0,0,0,0,0
Details by gene
Here you can find a tab-separated table.