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 |
|
A38 F1 I1 R1
|
17 |
54.1 |
3391312 |
97.1% |
3292963 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
4,179,865 |
A→C |
intergenic (+159/‑28) |
yjaG → / → hupA |
hypothetical protein/HU, DNA‑binding transcriptional regulator, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 4,179,865 | 0 | A | C | 98.2%
| 238.5
/ ‑4.1
| 56 | intergenic (+159/‑28) | yjaG/hupA | hypothetical protein/HU, DNA‑binding transcriptional regulator, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base C (21/34); total (21/35) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.66e-01 |
AAAAAAGTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCAAGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGAAAGCAG > REL606/4179792‑4179935
|
aaaaaaGTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGc < 1:531280/76‑1 (MQ=255)
aaaaGTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGa < 2:80108/76‑1 (MQ=255)
aaaGTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGAt > 2:500077/1‑76 (MQ=255)
aaaGTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGAt > 1:889832/1‑76 (MQ=255)
aGTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATaa < 1:380367/76‑1 (MQ=255)
gTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATaaa < 2:1213458/76‑1 (MQ=255)
gTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATaaa < 1:339083/76‑1 (MQ=255)
tGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAac > 2:594602/1‑76 (MQ=255)
ggCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAaca < 1:1524626/76‑1 (MQ=255)
cTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAAcaca < 2:237912/76‑1 (MQ=255)
tATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACAt > 2:907519/1‑76 (MQ=255)
ggTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTa > 2:833049/1‑76 (MQ=255)
ggTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTa > 2:1380707/1‑76 (MQ=255)
ggTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTa < 2:604580/76‑1 (MQ=255)
gTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTaa < 1:566653/76‑1 (MQ=255)
tGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAg < 2:479295/76‑1 (MQ=255)
gCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAgg > 1:1043706/1‑76 (MQ=255)
gtgtATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCAAGCGATAAACACATTGTAAGGAt < 1:1659864/76‑1 (MQ=255)
gtATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATaa > 1:1453630/1‑76 (MQ=255)
tATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAAc > 2:620905/1‑76 (MQ=255)
tATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAAc < 2:586749/76‑1 (MQ=255)
aTGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACt > 2:1640922/1‑76 (MQ=255)
aTGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACt > 1:250889/1‑76 (MQ=255)
tGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACtt < 2:665330/76‑1 (MQ=255)
tGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACtt < 2:1411086/76‑1 (MQ=255)
tGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACtt < 2:1347167/76‑1 (MQ=255)
gCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTa < 1:1133016/76‑1 (MQ=255)
cAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTAt < 2:1504847/76‑1 (MQ=255)
aGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATg < 1:581901/76‑1 (MQ=255)
aGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATg < 1:1318179/76‑1 (MQ=255)
agagTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAAc > 1:1381699/1‑76 (MQ=255)
gagTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACa < 1:1465820/76‑1 (MQ=255)
tGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGa < 2:588149/76‑1 (MQ=255)
tATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTc > 1:1193879/1‑76 (MQ=255)
tATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTc > 2:320242/1‑76 (MQ=255)
tATTCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTc > 2:1063839/1‑76 (MQ=255)
aTTCTGTCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCa < 1:83726/76‑1 (MQ=255)
ttCTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCaa < 2:1073140/76‑1 (MQ=255)
cTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACt < 2:1585575/76‑1 (MQ=255)
cTGGCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACt < 2:1478356/76‑1 (MQ=255)
ggCATTTCCGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAAAtga > 1:90336/1‑76 (MQ=255)
cGTCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTa < 1:1578494/76‑1 (MQ=255)
tCGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAAt < 1:111289/76‑1 (MQ=255)
cGCACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAAtt < 2:264394/76‑1 (MQ=255)
cACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGc < 2:634777/76‑1 (MQ=255)
cACTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGc < 1:214325/76‑1 (MQ=255)
aCTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACCCAACTGATTGATGTAATTGCa > 2:398871/1‑76 (MQ=255)
cTCGATGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCag < 2:250889/76‑1 (MQ=255)
aTGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGaa < 2:510996/76‑1 (MQ=255)
aTGCTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGaa > 2:323448/1‑76 (MQ=255)
cTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGAAAGc < 1:154234/76‑1 (MQ=255)
cTTAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGAAAGc > 1:955796/1‑76 (MQ=255)
ttAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGAAAGCa > 1:474615/1‑76 (MQ=255)
ttAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGAAAGCa > 2:161978/1‑76 (MQ=255)
ttAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGAAAGCa < 1:1656408/76‑1 (MQ=255)
tAGCACGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGAAAGCAg < 1:1094401/76‑1 (MQ=255)
|
AAAAAAGTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCAAGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGAAAGCAG > REL606/4179792‑4179935
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
