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 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,348,085 |
G→A |
38.6% |
E89K (GAA→AAA) |
npr → |
phosphohistidinoprotein‑hexose phosphotransferase component of N‑regulated PTS system (Npr) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,348,085 | 0 | G | A | 38.6%
| 35.8
/ 44.0
| 44 | E89K (GAA→AAA) | npr | phosphohistidinoprotein‑hexose phosphotransferase component of N‑regulated PTS system (Npr) |
| Reads supporting (aligned to +/- strand): ref base G (12/15); new base A (5/12); total (17/27) |
| Fisher's exact test for biased strand distribution p-value = 3.60e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAAGCGACCGGTCCACAGGAAGAGGAAGCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACAATAAGAAAATCACGTAC > W3110S.gb/3348016‑3348155
|
gaagCGACCGGTCCACAGGAAGAGGAAGCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTtgatg < 1:3177806/70‑1 (MQ=255)
cGACCGGTCCACAGGAAGAGGAAGCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGAt < 1:3021145/71‑1 (MQ=255)
ccGGTCCACAGGAAGAGGAAGCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTaa < 1:3681246/71‑1 (MQ=255)
cacaGGAAGAGGAAGCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTtca > 1:1401496/1‑71 (MQ=255)
ggaagaggaagCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTAATCTTCATCAc < 1:1690297/71‑1 (MQ=255)
agaggaagCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTAATCTtcatca > 1:4044519/1‑67 (MQ=255)
agaggaagCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTAATCTTCATCACttt < 1:530683/71‑1 (MQ=255)
agaggaagCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTAATCTTCATCACttt < 1:392791/71‑1 (MQ=255)
agaggaagCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTAATCTTCATCACttt < 1:387500/71‑1 (MQ=255)
gaggaagCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTg < 1:481201/71‑1 (MQ=255)
agCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATa > 1:2580726/1‑71 (MQ=255)
gCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATAc < 1:484355/71‑1 (MQ=255)
tGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGaa < 1:167620/41‑1 (MQ=255)
tGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGa < 1:4136553/43‑1 (MQ=255)
tGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTaa < 1:754313/47‑1 (MQ=255)
tGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTAATCTTCATCACTTTGa < 1:1194265/62‑1 (MQ=255)
tGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTAATCTTCATCACTTTGACATACAACt > 1:4383592/1‑71 (MQ=255)
ggCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTaa > 1:785506/1‑46 (MQ=255)
gccgTTATCGCCCTCTTTAATTCTGGTTTTGATAAAGATTAATCTTCATCACttt < 1:314910/55‑1 (MQ=255)
cgTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCa < 1:2475534/71‑1 (MQ=255)
ttATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTa < 1:652008/37‑1 (MQ=255)
ttATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATAc < 1:1110173/58‑1 (MQ=255)
tATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCAc > 1:2506021/1‑47 (MQ=255)
tATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCAc > 1:562776/1‑47 (MQ=255)
tATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCaaa > 1:1388036/1‑70 (MQ=255)
aTCTCCCTCTTTAATTCTGGTTTTGATAAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACt > 1:317115/1‑71 (MQ=255)
aTCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTtcatc > 1:51794/1‑44 (MQ=255)
aTCGCCCTCTTTAATTCTGGGTTTGATGAAGATTAATCTTCATCACTTTGACATACAACt < 1:4456388/60‑1 (MQ=255)
ctctTTAATTCTGGTTTTGATAAAGATTAATCTTCATCACTTTGACa < 1:2913938/47‑1 (MQ=255)
tctTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCa < 1:1888672/60‑1 (MQ=255)
ctTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCaaa > 1:1227151/1‑61 (MQ=255)
tttAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCaaa > 1:1367787/1‑60 (MQ=255)
tttAATTCTGGTTTTGATAAAGATTAATCTTCATCACttt < 1:1490812/40‑1 (MQ=255)
tttAATTCTGGTTTTGATAAAGATTAATCTTCATCACttt < 1:3372185/40‑1 (MQ=255)
ttAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACt > 1:4428723/1‑61 (MQ=255)
ttAATTCTGGTTTTGATAAAGATTAATCTtcatca > 1:1907901/1‑35 (MQ=255)
tAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACaa > 1:1562613/1‑47 (MQ=255)
tAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACaa > 1:3567184/1‑71 (MQ=255)
ttCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATaa < 1:717983/42‑2 (MQ=255)
ttCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACAATaa < 1:2042774/71‑1 (MQ=255)
cTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATAc < 1:4213071/40‑1 (MQ=255)
cTGGTTTTGATAAAGATTAATCTTCATCACTTTGa > 1:3046139/1‑35 (MQ=255)
ggTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACaa < 1:3510120/64‑1 (MQ=255)
gTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACAATAAGaaa < 1:2137730/70‑1 (MQ=255)
gTTTTGATAAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACAATAAGaa < 1:52463/69‑1 (MQ=255)
gatgaAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACAATAAGAAAATCAc < 1:3913297/70‑1 (MQ=255)
tgaAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACAATAAGAAAATCACGTa < 1:481409/71‑1 (MQ=255)
tgaAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACAATAAGAAAATCACGTa < 1:2837537/71‑1 (MQ=255)
gaAGATTAATCTTCATCACTTTGACATACAACTCCCTTCaaa > 1:3163823/1‑42 (MQ=255)
gaAGATTAATCTTCATCACTTTGACATACAACTCCCTTCaaa > 1:1728611/1‑42 (MQ=255)
gaAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACAATAAGAAAATCACGTAc > 1:3668509/1‑71 (MQ=255)
|
GAAGCGACCGGTCCACAGGAAGAGGAAGCACTGGCCGCCGTTATCGCCCTCTTTAATTCTGGTTTTGATGAAGATTAATCTTCATCACTTTGACATACAACTCCCTTCAAACTCCCCCCGACAATAAGAAAATCACGTAC > W3110S.gb/3348016‑3348155
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
