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 |
|
A5 F17 I0 R1
|
87 |
56.5 |
4283937 |
98.6% |
4223961 |
62.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,115,786 |
T→C |
8.1% |
intergenic (‑28/+55) |
msyB ← / ← mdtG |
hypothetical protein/predicted drug efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,115,786 | 0 | T | C | 8.1%
| 193.5
/ 9.5
| 74 | intergenic (‑28/+55) | msyB/mdtG | hypothetical protein/predicted drug efflux system |
| Reads supporting (aligned to +/- strand): ref base T (35/33); new base C (4/2); total (39/35) |
| Fisher's exact test for biased strand distribution p-value = 6.77e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.62e-01 |
AATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATACCTGG > W3110S.gb/1115726‑1115856
|
aaTGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCa > 1:1166849/1‑65 (MQ=255)
aaTGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAg > 1:3388935/1‑66 (MQ=255)
aaTGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaa > 1:1329271/1‑70 (MQ=255)
aaTGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTATCCCTTTGAGTTGATGAGGTTTCAg > 1:3707012/1‑66 (MQ=255)
aTGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaa > 1:2451634/1‑69 (MQ=255)
tGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGttt < 1:3382977/61‑1 (MQ=255)
tGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaa > 1:4178932/1‑68 (MQ=255)
gCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAgg < 1:3693838/70‑1 (MQ=255)
gCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAgg < 1:1062715/70‑1 (MQ=255)
cttcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGc > 1:350543/1‑71 (MQ=255)
cttcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGc > 1:3812036/1‑71 (MQ=255)
tcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCt > 1:1080150/1‑70 (MQ=255)
tcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCt < 1:2794045/70‑1 (MQ=255)
cAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAg < 1:1084126/67‑1 (MQ=255)
cAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCt < 1:1457313/69‑1 (MQ=255)
cAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGa > 1:112108/1‑71 (MQ=255)
cAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGa > 1:2450150/1‑71 (MQ=255)
aaGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGa < 1:3590015/70‑1 (MQ=255)
aaGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGAt > 1:4136709/1‑71 (MQ=255)
aGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGAtt < 1:4029254/71‑1 (MQ=255)
aGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGAtt < 1:2246081/71‑1 (MQ=255)
gCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATtc > 1:1001670/1‑71 (MQ=255)
cGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaaa > 1:1988680/1‑57 (MQ=255)
ttGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTcc > 1:423136/1‑71 (MQ=255)
tGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGAt > 1:2138081/1‑58 (MQ=255)
tGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGAt > 1:370800/1‑58 (MQ=255)
gTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCtt < 1:1299549/71‑1 (MQ=255)
tACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTc < 1:3798029/42‑1 (MQ=255)
cATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCtttt > 1:2306408/1‑70 (MQ=255)
aTGGTCTTCAAGATTGTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGc < 1:2224884/71‑1 (MQ=255)
aTGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGa > 1:3087248/1‑57 (MQ=255)
tGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCa > 1:927325/1‑39 (MQ=255)
tGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaaa > 1:1984384/1‑46 (MQ=255)
tGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGc < 1:2364064/70‑1 (MQ=255)
catcaCGATTCTCCCTTTGAGCTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAg < 1:2600102/69‑1 (MQ=255)
tcaCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGa < 1:936219/50‑1 (MQ=255)
tcaCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTAt < 1:1973568/70‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaa > 1:4058177/1‑37 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaa > 1:70852/1‑37 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGAt > 1:2089063/1‑42 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:482943/70‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:26166/70‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGaaa > 1:1426242/1‑37 (MQ=255)
cGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaaa < 1:770906/71‑1 (MQ=255)
cGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa > 1:1858795/1‑69 (MQ=255)
cGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATtctc > 1:2602307/1‑52 (MQ=255)
aTTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaaa < 1:2210689/69‑1 (MQ=255)
aTTCTCCCTTTGAGTTGATGAGGCTTCAGGGaaaat < 1:2790263/36‑2 (MQ=39)
aTTCTCCCTTTGAGTTGATGAGGCTTCAGGGaaaat < 1:1646426/36‑2 (MQ=39)
ctcCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCg > 1:3866733/1‑70 (MQ=255)
ccTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaaaa < 1:3882803/71‑1 (MQ=255)
ccTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaaaa < 1:532614/71‑1 (MQ=255)
cTTTGAGTTGATGAGGTTTCAGTGAAAAGGATAGCTGATTCTCCGCtttt < 1:100536/50‑1 (MQ=255)
cTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaaaaa > 1:125107/1‑71 (MQ=255)
ttGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCtttt > 1:2864166/1‑48 (MQ=255)
ttGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaa > 1:2481366/1‑59 (MQ=255)
ttGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAAt > 1:3663797/1‑70 (MQ=255)
tGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCtt > 1:934611/1‑45 (MQ=255)
tGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaaaa < 1:2529402/67‑1 (MQ=255)
tGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAAt > 1:217468/1‑69 (MQ=255)
tGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATc < 1:331458/70‑1 (MQ=255)
tGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATc < 1:1486322/70‑1 (MQ=255)
gTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:2789319/54‑1 (MQ=255)
gatgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaaaaa > 1:4157614/1‑62 (MQ=255)
gatgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCg < 1:891014/70‑1 (MQ=255)
gatgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGa > 1:1452430/1‑71 (MQ=255)
gatgaGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGa > 1:2137312/1‑71 (MQ=255)
atgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGAt < 1:1304201/71‑1 (MQ=255)
tgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGAt < 1:358209/70‑1 (MQ=255)
tgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATa > 1:2578768/1‑71 (MQ=255)
aGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaaa > 1:3599950/1‑49 (MQ=255)
gTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGc < 1:2633436/37‑1 (MQ=255)
gTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGc < 1:3531031/37‑1 (MQ=255)
gTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATACCTg < 1:3241166/71‑1 (MQ=255)
gTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATACCTg < 1:3256532/71‑1 (MQ=255)
tttCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATACCTgg < 1:3687297/71‑1 (MQ=255)
|
AATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATACCTGG > W3110S.gb/1115726‑1115856
|
| 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
