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 SAMPLE2_PE.vcf.gz -csvStats SAMPLE2_PE.snpeff.csv |
| Warnings | 6 |
| 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 | 49 |
| 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 | 1 | 2.041% | |
| LOW | 1 | 2.041% | |
| MODERATE | 6 | 12.245% | |
| MODIFIER | 41 | 83.673% |
| Type (alphabetical order) | Count | Percent | |
|---|---|---|---|
| MISSENSE | 6 | 85.714% | |
| SILENT | 1 | 14.286% |
Missense / Silent ratio: 6
| 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 | 0 | 0 |
| C | 0 | 0 | 0 | 4 |
| G | 0 | 0 | 0 | 1 |
| T | 1 | 1 | 0 | 0 |
Note: This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).
| Transitions | 5 |
|---|---|
| Transversions | 2 |
| Ts/Tv ratio | 2.5 |
All variants:
Sample ,SAMPLE2_PE,Total Transitions ,5,5 Transversions ,2,2 Ts/Tv ,2.500,2.500
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 , SAMPLE2_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).
| ACT | ATT | GAC | GAT | GCA | GGA | GTA | TAT | TCA | TTA | TTC | TTT | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ACT |   | 1 |   |   |   |   |   |   |   |   |   |   |
| ATT |   |   |   |   |   |   |   |   |   |   |   |   |
| GAC |   |   |   | 1 |   |   |   |   |   |   |   |   |
| GAT |   |   |   |   |   |   |   |   |   |   |   |   |
| GCA |   |   |   |   |   |   | 1 |   |   |   |   |   |
| GGA |   |   |   |   |   |   | 1 |   |   |   |   |   |
| GTA |   |   |   |   |   |   |   |   |   |   |   |   |
| TAT |   |   |   |   |   |   |   |   |   |   |   |   |
| TCA |   |   |   |   |   |   |   |   |   | 1 | 1 |   |
| TTA |   |   |   |   |   |   |   |   | 1 |   |   |   |
| 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 | D | F | G | I | L | S | T | V | Y | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| - |   | 1 |   |   |   |   |   |   |   |   |   |   |
| ? |   |   |   |   |   |   |   |   |   |   |   |   |
| A |   |   |   |   |   |   |   |   |   |   | 1 |   |
| D |   |   |   | 1 |   |   |   |   |   |   |   |   |
| F |   |   |   |   |   |   |   |   |   |   |   | 1 |
| G |   |   |   |   |   |   |   |   |   |   | 1 |   |
| I |   |   |   |   |   |   |   |   |   |   |   |   |
| L |   |   |   |   |   |   |   |   | 1 |   |   |   |
| S |   |   |   |   | 1 |   |   | 1 |   |   |   |   |
| T |   |   |   |   |   |   | 1 |   |   |   |   |   |
| V |   |   |   |   |   |   |   |   |   |   |   |   |
| Y |   |   |   |   |   |   |   |   |   |   |   |   |
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0
Details by gene
Here you can find a tab-separated table.