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 F3 I0 R2
|
260 |
44.3 |
3360226 |
90.5% |
3041004 |
64.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,773,435 |
T→C |
58.7% |
L488L (TTG→CTG) |
yfjW → |
predicted inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,773,435 | 0 | T | C | 58.7%
| 23.4
/ 52.0
| 46 | L488L (TTG→CTG) | yfjW | predicted inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base T (5/14); new base C (19/8); total (24/22) |
| Fisher's exact test for biased strand distribution p-value = 6.34e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.16e-01 |
TAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTTTGTTG > W3110S.gb/2773371‑2773501
|
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATg > 1:1233554/1‑71 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATg > 1:2181266/1‑71 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATg > 1:214655/1‑71 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATg > 1:697434/1‑71 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATg > 1:562025/1‑71 (MQ=255)
aGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:1876501/1‑68 (MQ=255)
aGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:2873433/1‑68 (MQ=255)
aGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:2951477/1‑68 (MQ=255)
aGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:1981438/1‑68 (MQ=255)
aGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:3350930/1‑68 (MQ=255)
aGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:61208/1‑68 (MQ=255)
aGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:847320/1‑68 (MQ=255)
aGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:1318327/1‑68 (MQ=255)
aGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:1287595/1‑68 (MQ=255)
cGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGt > 1:2898846/1‑69 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:445082/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:488285/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:2749756/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:3326105/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:3152161/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:3067423/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:909941/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:2896984/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:281743/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:2486172/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:1850945/59‑1 (MQ=255)
gAAACATTTGTCGTTAAGGACAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg < 1:950508/59‑1 (MQ=255)
aaCATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGa > 1:3277332/1‑59 (MQ=255)
aaCATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGa > 1:547098/1‑59 (MQ=255)
tGTCGTTAAGGCCAGAATCGGGGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCaa > 1:2098377/1‑70 (MQ=255)
tGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCaa > 1:233722/1‑70 (MQ=255)
ggAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGca > 1:2728294/1‑71 (MQ=255)
ggAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGca > 1:1683598/1‑71 (MQ=255)
ggAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGca > 1:2327563/1‑71 (MQ=255)
attattTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCAcagcag < 1:1855337/70‑1 (MQ=255)
attattTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCAcagcag < 1:1763813/70‑1 (MQ=255)
ttattTCTGAAGGGAGTCTGTATGGACTAGTtaataa < 1:1229407/37‑1 (MQ=255)
ttattTCTGAAGGGAGTCTGTATGGACTAGTtaataa < 1:3327526/37‑1 (MQ=255)
ttattTCTGAAGGGAGTCTGTATGGACTAGTtaataa < 1:1941270/37‑1 (MQ=255)
ttattTCTGAAGGGAGTCTGTATGGACTAGTtaataa < 1:196591/37‑1 (MQ=255)
ttattTCTGAAGGGAGTCTGTATGGACTAGTtaataa < 1:1752332/37‑1 (MQ=255)
ttattTCTGAAGGGAGTCTGTATGGACTAGTtaataa < 1:680108/37‑1 (MQ=255)
ttattTCTGAAGGGAGTCTGTATGGACTAGTtaataa < 1:237229/37‑1 (MQ=255)
ttattTCTGAAGGGAGTCTGTATGGACTAGTtaataa < 1:1520646/37‑1 (MQ=255)
gAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatata > 1:1765066/1‑45 (MQ=255)
gAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatata > 1:13255/1‑45 (MQ=255)
tttGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTttgttg < 1:661063/68‑1 (MQ=255)
tttGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTttgttg < 1:2757888/68‑1 (MQ=255)
|
TAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTTTGTTG > W3110S.gb/2773371‑2773501
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
