SnpEff: Variant analysis
Genome | nCoV-2019.reference |
Date | 2024-04-26 12:25 |
SnpEff version | SnpEff 5.0e (build 2021-03-09 06:01), by Pablo Cingolani |
Command line arguments | SnpEff nCoV-2019.reference SAMPLE1_PE.vcf.gz -csvStats SAMPLE1_PE.snpeff.csv |
Warnings | 9 |
Errors | 0 |
Number of lines (input file) | 8 |
Number of variants (before filter) | 8 |
Number of not variants (i.e. reference equals alternative) |
0 |
Number of variants processed (i.e. after filter and non-variants) |
8 |
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 | 26 |
Genome total length | 29,903 |
Genome effective length | 29,903 |
Variant rate | 1 variant every 3,737 bases |
Chromosome | Length | Variants | Variants rate |
---|---|---|---|
MN908947.3 | 29,903 | 8 | 3,737 |
Total | 29,903 | 8 | 3,737 |
Type | Total |
---|---|
SNP | 7 |
MNP | 0 |
INS | 1 |
DEL | 0 |
MIXED | 0 |
INV | 0 |
DUP | 0 |
BND | 0 |
INTERVAL | 0 |
Total | 8 |
Type (alphabetical order) | Count | Percent | |
---|---|---|---|
HIGH | 2 | 7.692% | |
LOW | 3 | 11.538% | |
MODERATE | 2 | 7.692% | |
MODIFIER | 19 | 73.077% |
Type (alphabetical order) | Count | Percent | |
---|---|---|---|
MISSENSE | 3 | 50% | |
SILENT | 3 | 50% |
Missense / Silent ratio: 1
Type | Region | ||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
Quality:
Insertions and deletions length:
Min | 0 |
---|---|
Max | 0 |
Mean | 0 |
Median | 0 |
Standard deviation | 0 |
Values | 0 |
Count | 1 |
A | C | G | T | |
---|---|---|---|---|
A | 0 | 0 | 2 | 0 |
C | 0 | 0 | 0 | 4 |
G | 1 | 0 | 0 | 0 |
T | 0 | 0 | 0 | 0 |
Note: This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).
Transitions | 7 |
---|---|
Transversions | 0 |
Ts/Tv ratio | 0 |
All variants:
Sample ,SAMPLE1_PE,Total Transitions ,7,7 Transversions ,0,0 Ts/Tv ,Infinity,Infinity
Only known variants (i.e. the ones having a non-empty ID field):
No results available (empty input?)
Min | 50 |
---|---|
Max | 50 |
Mean | 50 |
Median | 50 |
Standard deviation | 0 |
Values | 50 |
Count | 8 |
Min | 1 |
---|---|
Max | 1 |
Mean | 1 |
Median | 1 |
Standard deviation | 0 |
Values | 1 |
Count | 8 |
Sample_names , SAMPLE1_PE Reference , 0 Het , 8 Hom , 0 Missing , 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).
CAA | CAG | CTA | GAT | GCA | GGT | GTA | TAG | TCA | TGG | TTA | TTC | TTT | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CAA |   |   |   |   |   |   |   |   |   |   |   |   |   |
CAG | 1 |   |   |   |   |   |   |   |   |   |   |   |   |
CTA |   |   |   |   |   |   |   |   |   |   | 1 |   |   |
GAT |   |   |   |   |   | 1 |   |   |   |   |   |   |   |
GCA |   |   |   |   |   |   | 1 |   |   |   |   |   |   |
GGT |   |   |   |   |   |   |   |   |   |   |   |   |   |
GTA |   |   |   |   |   |   |   |   |   |   |   |   |   |
TAG |   |   |   |   |   |   |   |   |   | 1 |   |   |   |
TCA |   |   |   |   |   |   |   |   |   |   |   | 1 |   |
TGG |   |   |   |   |   |   |   |   |   |   |   |   |   |
TTA |   |   |   |   |   |   |   |   |   |   |   |   |   |
TTC |   |   |   |   |   |   |   |   |   |   |   |   | 1 |
TTT |   |   |   |   |   |   |   |   |   |   |   |   |   |
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 | D | F | G | L | Q | S | V | W | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
* |   |   |   |   |   |   |   |   |   |   |   | 1 |
- |   |   | 1 |   |   |   |   |   |   |   |   |   |
? |   |   |   |   |   |   |   |   |   |   |   |   |
A |   |   |   |   |   |   |   |   |   |   | 1 |   |
D |   |   |   |   |   |   | 1 |   |   |   |   |   |
F |   |   |   |   |   | 1 |   |   |   |   |   |   |
G |   |   |   |   |   |   |   |   |   |   |   |   |
L |   |   |   |   |   |   |   | 1 |   |   |   |   |
Q |   |   |   |   |   |   |   |   | 1 |   |   |   |
S |   |   |   |   |   | 1 |   |   |   |   |   |   |
V |   |   |   |   |   |   |   |   |   |   |   |   |
W |   |   |   |   |   |   |   |   |   |   |   |   |
MN908947.3, Position,0,100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500,1600,1700,1800,1900,2000,2100,2200,2300,2400,2500,2600,2700,2800,2900,3000,3100,3200,3300,3400,3500,3600,3700,3800,3900,4000,4100,4200,4300,4400,4500,4600,4700,4800,4900,5000,5100,5200,5300,5400,5500,5600,5700,5800,5900,6000,6100,6200,6300,6400,6500,6600,6700,6800,6900,7000,7100,7200,7300,7400,7500,7600,7700,7800,7900,8000,8100,8200,8300,8400,8500,8600,8700,8800,8900,9000,9100,9200,9300,9400,9500,9600,9700,9800,9900,10000,10100,10200,10300,10400,10500,10600,10700,10800,10900,11000,11100,11200,11300,11400,11500,11600,11700,11800,11900,12000,12100,12200,12300,12400,12500,12600,12700,12800,12900,13000,13100,13200,13300,13400,13500,13600,13700,13800,13900,14000,14100,14200,14300,14400,14500,14600,14700,14800,14900,15000,15100,15200,15300,15400,15500,15600,15700,15800,15900,16000,16100,16200,16300,16400,16500,16600,16700,16800,16900,17000,17100,17200,17300,17400,17500,17600,17700,17800,17900,18000,18100,18200,18300,18400,18500,18600,18700,18800,18900,19000,19100,19200,19300,19400,19500,19600,19700,19800,19900,20000,20100,20200,20300,20400,20500,20600,20700,20800,20900,21000,21100,21200,21300,21400,21500,21600,21700,21800,21900,22000,22100,22200,22300,22400,22500,22600,22700,22800,22900,23000,23100,23200,23300,23400,23500,23600,23700,23800,23900,24000,24100,24200,24300,24400,24500,24600,24700,24800,24900,25000,25100,25200,25300,25400,25500,25600,25700,25800,25900,26000,26100,26200,26300,26400,26500,26600,26700,26800,26900,27000,27100,27200,27300,27400,27500,27600,27700,27800,27900,28000,28100,28200,28300,28400,28500,28600,28700,28800,28900,29000,29100,29200,29300,29400,29500,29600,29700,29800,29900 MN908947.3,Count,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
Details by gene
Here you can find a tab-separated table.