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 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

Variants rate details

Chromosome Length Variants Variants rate
22 51,353,906 144,424 355
Total 51,353,906 144,424 355

Number variants by type

Type Total
SNP 144,292
MNP 0
INS 84
DEL 48
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 144,424

Number of effects by impact

Type (alphabetical order)   Count Percent
MODIFIER   144,424 100%

Number of effects by functional class

Type (alphabetical order)   Count Percent

Missense / Silent ratio: 0

Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
intergenic_region   144,424 100%

Type (alphabetical order)   Count Percent
INTERGENIC   144,424 100%

Quality: 

	

		
 Min3 

		
 Max150 

		
 Mean139.724 

		
 Median150 

		
 Standard deviation24.672 

		
 Values3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,29,30,39,48,50,58,69,80,82,90,140,150 

		
 Count15,2,30,36,2,1,9,11,1,5,15,1,4,5,5,9,3,20,6,3,12,19,24,10,1230,2,15,1,1,1,16757,1,8749,8944,155810
Insertions and deletions length: 

	

		
 Min0 

		
 Max271 

		
 Mean8.856 

		
 Median1 

		
 Standard deviation32.008 

		
 Values0,1,2,3,4,5,6,7,8,9,10,11,12,13,15,20,27,30,58,176,271 

		
 Count31,54,3,3,1,2,1,1,2,7,4,7,4,2,3,1,1,1,1,2,1
Base changes (SNPs)

  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

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 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?)
Allele frequency


Min1
Max100
Mean72.398
Median84
Standard deviation24.858
Values1,2,3,5,6,7,8,10,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,28,29,30,31,32,33,34,35,37,38,39,40,41,42,43,44,45,46,47,48,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,96,97,98,100
Count200,4825,38,2632,30,2107,14,647,16,1014,15,7,2034,2,1144,16,5,752,8,387,3,1187,9,225,6,410,2,4,464,11,359,3,58,15,1,510,13,569,16,1,702,4,178,33,1286,21,691,3,26,1044,5,313,1,6,317,8,4,257,9,639,16,13,1329,4,565,4,27,3423,13,2670,28,2749,18,39,2699,135,104024,170,40,30,36,18,25,46,14,15,7,10,7,6

Allele Count


Min1
Max78
Mean56.909
Median66
Standard deviation19.421
Values1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78
Count200,4826,37,2636,26,2108,13,647,16,1030,7,2035,2,1163,5,755,5,387,3,1191,5,226,5,412,4,470,5,361,2,71,4,519,5,581,4,709,1,204,6,1300,8,711,5,1049,1,328,1,323,7,265,4,678,15,1343,2,570,12,3433,12,2670,21,2831,18,2833,54,103937,170,30,32,13,25,46,13,13,7,8,7,5

Hom/Het per sample 




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

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).

 

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).

 

Variants by chromosome

		

		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.