SnpEff: Variant analysis
Genome | ebola_zaire |
Date | 2020-12-02 10:35 |
SnpEff version | SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani |
Command line arguments | SnpEff ebola_zaire -s all_effects_report.html |
Warnings | 0 |
Errors | 0 |
Number of lines (input file) | 24 |
Number of variants (before filter) | 24 |
Number of not variants (i.e. reference equals alternative) |
0 |
Number of variants processed (i.e. after filter and non-variants) |
24 |
Number of known variants (i.e. non-empty ID) |
0 ( 0% ) |
Number of multi-allelic VCF entries (i.e. more than two alleles) |
0 |
Number of effects | 117 |
Genome total length | 18,959 |
Genome effective length | 18,959 |
Variant rate | 1 variant every 789 bases |
Chromosome | Length | Variants | Variants rate |
---|---|---|---|
KJ660346 | 18,959 | 24 | 789 |
Total | 18,959 | 24 | 789 |
Type | Total |
---|---|
SNP | 24 |
MNP | 0 |
INS | 0 |
DEL | 0 |
MIXED | 0 |
INV | 0 |
DUP | 0 |
BND | 0 |
INTERVAL | 0 |
Total | 24 |
Type (alphabetical order) | Count | Percent | |
---|---|---|---|
LOW | 12 | 10.256% | |
MODERATE | 12 | 10.256% | |
MODIFIER | 93 | 79.487% |
Type (alphabetical order) | Count | Percent | |
---|---|---|---|
MISSENSE | 12 | 50% | |
SILENT | 12 | 50% |
Missense / Silent ratio: 1
Type | Region | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
Quality:
Min | 3 |
---|---|
Max | 670 |
Mean | 260 |
Median | 135 |
Standard deviation | 257.674 |
Values | 3,4,22,23,51,95,108,162,353,430,463,472,484,509,571,587,604,612,670 |
Count | 4,3,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 |
Insertions and deletions length:
A | C | G | T | |
---|---|---|---|---|
A | 0 | 2 | 3 | 0 |
C | 1 | 0 | 0 | 5 |
G | 5 | 0 | 0 | 2 |
T | 1 | 4 | 1 | 0 |
Note: This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).
Transitions | 35 |
---|---|
Transversions | 11 |
Ts/Tv ratio | 3.1818 |
All variants:
Sample ,bam/SRR1972917.bam,bam/SRR1972918.bam,bam/SRR1972919.bam,bam/SRR1972920.bam,bam/SRR1972921.bam,Total Transitions ,10,10,2,3,10,35 Transversions ,4,2,3,1,1,11 Ts/Tv ,2.500,5.000,0.667,3.000,10.000,3.182
Only known variants (i.e. the ones having a non-empty ID field):
No results available (empty input?)
Min | 10 |
---|---|
Max | 50 |
Mean | 28.042 |
Median | 20.5 |
Standard deviation | 16.897 |
Values | 10,12,16,25,30,33,50 |
Count | 2,5,5,2,1,1,8 |
Min | 1 |
---|---|
Max | 5 |
Mean | 1.917 |
Median | 1 |
Standard deviation | 1.213 |
Values | 1,2,3,4,5 |
Count | 13,4,4,2,1 |
Sample_names , bam/SRR1972917.bam, bam/SRR1972918.bam, bam/SRR1972919.bam, bam/SRR1972920.bam, bam/SRR1972921.bam Reference , 5, 12, 2, 7, 13 Het , 14, 12, 5, 4, 11 Hom , 0, 0, 0, 0, 0 Missing , 5, 0, 17, 13, 0
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).
AAA | AAG | AGC | ATA | ATC | ATG | ATT | CAA | CAG | CCA | CCC | CCT | CGT | CTA | CTG | GAC | GAT | GCA | GCG | GTA | GTC | GTG | GTT | TGT | TTC | TTT | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
AAA |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
AAG | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
AGC |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
ATA |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
ATC |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
ATG |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
ATT |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
CAA |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
CAG |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
CCA |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
CCC |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
CCT |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
CGT |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |
CTA |   |   |   |   |   |   |   |   |   | 3 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
CTG |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |
GAC |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
GAT |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |
GCA |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |
GCG |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 3 |   |   |   |   |
GTA |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |
GTC |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | 3 |   |   |   |
GTG |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
GTT |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |
TGT |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
TTC |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
TTT |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |
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).
A | C | D | F | I | K | L | M | P | Q | R | S | V | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A |   |   |   |   |   |   |   |   |   |   |   |   | 4 |
C |   |   |   |   |   |   |   |   |   |   |   |   |   |
D |   |   | 1 |   |   |   |   |   |   |   |   |   |   |
F |   |   |   | 1 |   |   |   |   |   |   |   |   |   |
I |   |   |   |   | 1 |   |   |   |   |   |   |   |   |
K |   |   |   |   |   | 1 |   |   |   |   |   |   |   |
L |   |   |   |   |   |   | 1 |   | 3 |   |   |   |   |
M |   |   |   |   | 1 |   |   |   |   |   |   |   |   |
P |   |   |   |   |   |   |   |   | 2 |   |   |   |   |
Q |   |   |   |   |   |   |   |   |   | 1 |   |   |   |
R |   | 1 |   |   |   |   |   |   |   |   |   |   |   |
S |   |   |   |   | 1 |   |   |   |   |   |   |   |   |
V |   |   | 1 | 1 |   |   |   |   |   |   |   |   | 4 |
KJ660346, Position,0,100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500,1600,1700,1800,1900,2000,2100,2200,2300,2400,2500,2600,2700,2800,2900,3000,3100,3200,3300,3400,3500,3600,3700,3800,3900,4000,4100,4200,4300,4400,4500,4600,4700,4800,4900,5000,5100,5200,5300,5400,5500,5600,5700,5800,5900,6000,6100,6200,6300,6400,6500,6600,6700,6800,6900,7000,7100,7200,7300,7400,7500,7600,7700,7800,7900,8000,8100,8200,8300,8400,8500,8600,8700,8800,8900,9000,9100,9200,9300,9400,9500,9600,9700,9800,9900,10000,10100,10200,10300,10400,10500,10600,10700,10800,10900,11000,11100,11200,11300,11400,11500,11600,11700,11800,11900,12000,12100,12200,12300,12400,12500,12600,12700,12800,12900,13000,13100,13200,13300,13400,13500,13600,13700,13800,13900,14000,14100,14200,14300,14400,14500,14600,14700,14800,14900,15000,15100,15200,15300,15400,15500,15600,15700,15800,15900,16000,16100,16200,16300,16400,16500,16600,16700,16800,16900,17000,17100,17200,17300,17400,17500,17600,17700,17800,17900,18000,18100,18200,18300,18400,18500,18600,18700,18800,18900 KJ660346,Count,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,1,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,1,0,0,0,1,0,0,1,0,0,0,0,0,0,1,0,1,0,1,0,0,0,0
Details by gene
Here you can find a tab-separated table.