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 |
2,160,543 |
C→T |
42.6% |
F7F (TTC→TTT) |
mdtC → |
multidrug efflux system, subunit C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,160,543 | 0 | C | T | 42.6%
| 19.7
/ 54.5
| 47 | F7F (TTC→TTT) | mdtC | multidrug efflux system, subunit C |
| Reads supporting (aligned to +/- strand): ref base C (15/12); new base T (10/10); total (25/22) |
| Fisher's exact test for biased strand distribution p-value = 7.73e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.53e-01 |
GTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCGG > W3110S.gb/2160480‑2160596
|
gtgGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTAcc > 1:2770605/1‑71 (MQ=255)
gtgGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTAcc > 1:2428301/1‑71 (MQ=255)
tGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGAttt > 1:822411/1‑71 (MQ=255)
tGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGAttt > 1:1347886/1‑71 (MQ=255)
aTGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCg > 1:1641376/1‑71 (MQ=255)
tGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGc < 1:2941197/54‑1 (MQ=255)
aaGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCg > 1:2746558/1‑43 (MQ=255)
aaGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGcga > 1:1005887/1‑54 (MQ=255)
aaGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGcga > 1:1117198/1‑54 (MQ=255)
aaGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGcga > 1:2872154/1‑54 (MQ=255)
aggaggCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTTCTGTCGGTTGc < 1:2253540/70‑1 (MQ=255)
aggCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCAtt < 1:989268/71‑1 (MQ=255)
aggCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCAtt < 1:3156745/71‑1 (MQ=255)
aggCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCAtt < 1:2313104/71‑1 (MQ=255)
aggCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCAtt < 1:2226700/71‑1 (MQ=255)
aggCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCAtt < 1:1586309/71‑1 (MQ=255)
ggCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCAtt < 1:2773439/70‑1 (MQ=255)
gCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTAc < 1:2008603/71‑1 (MQ=255)
gCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTAc < 1:952892/71‑1 (MQ=255)
gCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTAc < 1:2953547/71‑1 (MQ=255)
gCGTAAGTGAAGTTTTTTGCACTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTTCCATTAc < 1:539903/71‑1 (MQ=255)
tAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTAc < 1:2444203/68‑1 (MQ=255)
tAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTAc < 1:2505590/68‑1 (MQ=255)
aGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTAc < 1:419131/66‑1 (MQ=255)
gTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGc < 1:1073992/59‑1 (MQ=255)
gTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGc < 1:1124809/59‑1 (MQ=255)
gTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGc < 1:688181/59‑1 (MQ=255)
gTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGc < 1:1778943/59‑1 (MQ=255)
gTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGc < 1:2262086/59‑1 (MQ=255)
gTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGc < 1:1639252/59‑1 (MQ=255)
gTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGc < 1:2398216/59‑1 (MQ=255)
gAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCa > 1:1126111/1‑59 (MQ=255)
gAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCa > 1:3312859/1‑59 (MQ=255)
gAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCa > 1:1235687/1‑59 (MQ=255)
gAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCa > 1:1300015/1‑59 (MQ=255)
gAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCa > 1:1498757/1‑59 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTa > 1:2524349/1‑61 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCgg > 1:2919033/1‑71 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCgg > 1:1276668/1‑71 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCgg > 1:2999240/1‑71 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCgg > 1:2459040/1‑71 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCgg > 1:2353964/1‑71 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCgg > 1:794628/1‑71 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCgg > 1:1750802/1‑71 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCgg > 1:960323/1‑71 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCg > 1:2298350/1‑70 (MQ=255)
aaGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCg > 1:2533617/1‑70 (MQ=255)
|
GTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCGG > W3110S.gb/2160480‑2160596
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
