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 |
|
A2 F3 I0 R1
|
328 |
90.1 |
2317887 |
85.2% |
1974839 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
755,969 |
C→G |
100% |
V32V (GTC→GTG) |
lolD → |
outer membrane‑specific lipoprotein transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 755,969 | 0 | C | G | 84.1%
| 108.0
/ 15.3
| 44 | V32V (GTC→GTG) | lolD | outer membrane‑specific lipoprotein transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (6/1); new base G (0/37); total (6/38) |
| Fisher's exact test for biased strand distribution p-value = 9.92e-07 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.77e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CAAACCGATGTGCTGCACAATGTCAGTTTCAGCGTCGGCGAAGGTGAAATGATGGCGATCGTCGGTAGCTCTGGTTCCGGTA > minE/755934‑756015
|
cAAACCGATGTGCTGCACAATGTCAGTTTCAGCGTCGGCGAAGGTGAAat < 1:2279322/50‑1 (MQ=255)
aaCCGATGTGCTGCACAATGTCAGTTTCAGCGTCGGCGAAGGTGAAATGATGGCg > 1:1038025/1‑55 (MQ=255)
aaCCGATGTGCTGCACAATGTCAGTTTCAGCGTCGGCGAAGGTGAAATGATGGCg > 1:2228648/1‑55 (MQ=255)
aaCCGATGTGCTGCACAATGTCAGTTTCAGCGTCGGCGAAGGTGAAATGATGGCg > 1:1325317/1‑55 (MQ=255)
aaCCGATGTGCTGCACAATGTCAGTTTCAGCGTCGGCGAAGGTGAAATGATGGCg > 1:883225/1‑55 (MQ=255)
aaCCGATGTGCTGCACAATGTCAGTTTCAGCGTCGGCGAAGGTGAAATGATGGCg > 1:466741/1‑55 (MQ=255)
aaCAGATGTGCTGCACAATGTCAGTTTCAGCGTCGGc > 1:444745/1‑37 (MQ=255)
tCAGCGTGGTCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1698844/54‑1 (MQ=38)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:2206781/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:2105006/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:2212825/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:346036/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:371476/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:446080/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:515292/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:586749/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:59832/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:676751/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:820387/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:823148/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:900776/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:960248/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:983947/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:2131158/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1171793/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1201039/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:124844/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1398850/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1419188/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1498000/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1565690/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1622591/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:162896/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:170723/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1713030/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1812553/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1839470/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1924209/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1943004/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:2016836/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:2101819/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1037590/54‑1 (MQ=39)
tCAGCGTGGGCGAAGGTGAAATGATGGCGATCGGCGGCAGCTCTGGTTCCGGTa < 1:995987/54‑1 (MQ=255)
cAGCGTGGGCGAAGGTGAAATGATGGCGATCGTCGGCAGCTCTGGTTCCGGTa < 1:1692050/53‑1 (MQ=39)
|
CAAACCGATGTGCTGCACAATGTCAGTTTCAGCGTCGGCGAAGGTGAAATGATGGCGATCGTCGGTAGCTCTGGTTCCGGTA > minE/755934‑756015
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
