Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F1 I1 R1
|
66 |
46.7 |
5280542 |
98.1% |
5180211 |
47.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,116,106 |
2 bp→CG |
pseudogene (1347‑1348/2509 nt) |
vgrG → |
type VI secretion system tip protein VgrG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,116,106 | 0 | N | C | 100.0%
| 13.8
/ NA
| 5 | pseudogene (1347/2509 nt) | vgrG | type VI secretion system tip protein VgrG |
| Reads supporting (aligned to +/- strand): ref base N (0/0); new base C (2/3); total (2/3) |
| * | NC_017635 | 3,116,107 | 0 | C | G | 100.0%
| 14.6
/ NA
| 5 | pseudogene (1348/2509 nt) | vgrG | type VI secretion system tip protein VgrG |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (2/3); total (2/3) |
GTCAGCATCGNCTTTGAGGAAGGCAACCCGGACCGACCTTATATCGCAGGC > NC_017635/3116096‑3116146
||
gTCAGCATCGCGTTTGAGGAAGGCAACCCGGACCGACCTTATATCg > 1:137962/1‑46 (MQ=255)
tCAGCATCGCGTTTGAGGAAGGCAACCCGGACCGACCTTATATCGCAg < 1:8307/48‑1 (MQ=255)
tCAGCATCGCGTTTGAGGAAGGCAACCCGGACCGACCTTATATCGCAg < 2:649983/48‑1 (MQ=255)
cAGCATCGCGTTTGAGGAAGGCAACCCGGACCGACCTTATATCGCAgg > 2:948599/1‑48 (MQ=255)
aGCATCGCGTTTGAGGAAGGCAACCCGGACCGACCTTATATCGCAGGc < 2:767104/48‑1 (MQ=255)
||
GTCAGCATCGNCTTTGAGGAAGGCAACCCGGACCGACCTTATATCGCAGGC > NC_017635/3116096‑3116146
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
