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 |
|
A6 F17 I0 R2
|
159 |
90.8 |
4763082 |
92.7% |
4415377 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,736,671 |
T→C |
8.4% |
F605F (TTT→TTC) |
fusA → |
protein chain elongation factor EF‑G |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,736,671 | 0 | T | C | 8.4%
| 238.2
/ 11.6
| 83 | F605F (TTT→TTC) | fusA | protein chain elongation factor EF‑G |
| Reads supporting (aligned to +/- strand): ref base T (23/53); new base C (3/4); total (26/57) |
| Fisher's exact test for biased strand distribution p-value = 6.72e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.01e-01 |
TTACCATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAGAGAACACCG > minE/2736602‑2736741
|
ttACCATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCttt > 1:4300890/1‑70 (MQ=255)
ttACCATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCttt > 1:2120818/1‑70 (MQ=255)
aCCATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCttt < 1:3874970/68‑1 (MQ=255)
aCCATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCttt < 1:3426484/68‑1 (MQ=255)
aCCATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCttt > 1:3229698/1‑68 (MQ=255)
aCCATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTaa < 1:4321569/70‑1 (MQ=255)
ccATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAg < 1:3349788/70‑1 (MQ=255)
ccATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAg < 1:3344185/70‑1 (MQ=255)
ccATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGa < 1:4458965/71‑1 (MQ=255)
ccATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGa < 1:1807308/71‑1 (MQ=255)
aTGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGa > 1:3871842/1‑69 (MQ=255)
aTGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGa > 1:740451/1‑69 (MQ=255)
aCGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGc < 1:1230447/70‑1 (MQ=255)
aCGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGc < 1:3985811/70‑1 (MQ=255)
aCGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGc < 1:3034790/70‑1 (MQ=255)
aCGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGc < 1:4682761/70‑1 (MQ=255)
cGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGa < 1:4714735/71‑1 (MQ=255)
cGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGa < 1:4311322/71‑1 (MQ=255)
gTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGaa < 1:720092/71‑1 (MQ=255)
gTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGaa < 1:447230/71‑1 (MQ=255)
gTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGaa < 1:292611/71‑1 (MQ=255)
gTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTCAAGAAAGCGaa < 1:3346732/71‑1 (MQ=255)
gTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTCAAGAAAGCGaa < 1:2708253/71‑1 (MQ=255)
tGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGaaa > 1:2886503/1‑70 (MQ=255)
aCTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAAcc < 1:4314950/70‑1 (MQ=255)
aCTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAAcc < 1:568557/70‑1 (MQ=255)
aCTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAAcc < 1:3162147/70‑1 (MQ=255)
ctcctcTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAACCGAAACCAg < 1:3984118/71‑1 (MQ=255)
ctctGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGaaa > 1:3002507/1‑64 (MQ=255)
ctctGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGtt < 1:578947/70‑1 (MQ=255)
ctctGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGtt < 1:852777/70‑1 (MQ=255)
ctctGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTc > 1:1323040/1‑71 (MQ=255)
ctctGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTc > 1:4363191/1‑71 (MQ=255)
ctctGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTc > 1:762084/1‑71 (MQ=255)
ctctGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTCAAGAAAGCGAAACCAGTTc > 1:2605767/1‑71 (MQ=255)
tGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCt < 1:1719994/69‑1 (MQ=255)
tGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCt < 1:4293002/69‑1 (MQ=255)
tGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCt < 1:4287273/69‑1 (MQ=255)
aaCTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTg < 1:4361452/68‑1 (MQ=255)
aaCTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCtt > 1:1273874/1‑71 (MQ=255)
cTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGa < 1:4200285/71‑1 (MQ=255)
tGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAg < 1:3714356/47‑1 (MQ=255)
gTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGa < 1:2779037/71‑1 (MQ=255)
gTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGa < 1:2488361/71‑1 (MQ=255)
tAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGaa > 1:4272651/1‑42 (MQ=255)
tAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGtt > 1:3205655/1‑55 (MQ=255)
tAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCa > 1:843536/1‑71 (MQ=255)
tAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCa > 1:2101494/1‑71 (MQ=255)
tAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCa > 1:1740863/1‑71 (MQ=255)
aaaCTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCa > 1:753114/1‑70 (MQ=255)
aaaCTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCa < 1:2937360/70‑1 (MQ=255)
aaCTGGCTGCTTCTATCGCCTTTAAAGAAGGCttt < 1:2694961/35‑1 (MQ=255)
aaCTGGCTGCTTCTATCGCCTTTAAAGAAGGCttt < 1:4132566/35‑1 (MQ=255)
aaCTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCAt < 1:1098071/70‑1 (MQ=255)
cTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGaa < 1:1697784/71‑1 (MQ=255)
tGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAAcc < 1:1948813/46‑1 (MQ=255)
tgctTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTg < 1:3752490/53‑1 (MQ=255)
tgctTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTg < 1:3813371/53‑1 (MQ=255)
tgctTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTg < 1:2075062/53‑1 (MQ=255)
tgctTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTg < 1:4614000/53‑1 (MQ=255)
tgctTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGtt < 1:1070733/70‑1 (MQ=255)
ctTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAg > 1:3108033/1‑53 (MQ=255)
ctTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAg > 1:1761220/1‑53 (MQ=255)
ctTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGa < 1:2321089/70‑1 (MQ=255)
ttCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGa < 1:3877872/62‑1 (MQ=255)
tCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGa < 1:4719035/70‑1 (MQ=255)
tCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGa < 1:440015/70‑1 (MQ=255)
tCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGa < 1:3582854/70‑1 (MQ=255)
tCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGa < 1:1806315/70‑1 (MQ=255)
tCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGa < 1:1382490/70‑1 (MQ=255)
tCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGa < 1:3721262/70‑1 (MQ=255)
tCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGa < 1:1260124/70‑1 (MQ=255)
cTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTc > 1:312741/1‑71 (MQ=255)
tttAAAGAAGGCTTCAAGAAAGCGAAACCAGTTCTg < 1:3366362/36‑1 (MQ=255)
tttAAAGAAGGCTTCAAGAAAGCGAAACCAGTTCTg < 1:3018796/36‑1 (MQ=255)
ttAATGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATg < 1:761983/50‑1 (MQ=255)
tAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATc > 1:3732437/1‑46 (MQ=255)
tAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATc > 1:938806/1‑46 (MQ=255)
tAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCg > 1:3622385/1‑70 (MQ=255)
tAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCg > 1:598413/1‑70 (MQ=255)
tAAAGAAGGCTTCAAGAAAGCGAAACCAGTTCTGCt > 1:168639/1‑36 (MQ=255)
tAAAGAAGGCTTCAAGAAAGCGAAACCAGTTCTGCTTGAGCAGATCATGAAGGTTGAAGTAGAAACTCCg > 1:3918212/1‑70 (MQ=255)
aagaagGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGaa < 1:2766499/71‑1 (MQ=255)
aagaagGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGa < 1:2652365/70‑1 (MQ=255)
aagGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAagag < 1:200647/71‑1 (MQ=255)
agGCTTTAAGGAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAagag > 1:4735057/1‑70 (MQ=255)
agGCTTTAAGATAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAgaga < 1:2364191/71‑1 (MQ=255)
ggCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAGAGaa < 1:1940741/71‑1 (MQ=255)
ggCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAGAGaa < 1:389187/71‑1 (MQ=255)
gCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAGAGaa > 1:914395/1‑70 (MQ=255)
ttAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCAt < 1:635194/37‑1 (MQ=255)
ttAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCAt < 1:4387584/37‑1 (MQ=255)
tAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAgaga > 1:1939508/1‑65 (MQ=255)
tAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAgaga > 1:3434812/1‑65 (MQ=255)
tAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAGAGAACACCg > 1:4505394/1‑71 (MQ=255)
|
TTACCATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCCTTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAGAGAACACCG > minE/2736602‑2736741
|
| 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
