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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
837,728 |
C→G |
22.4% |
F67L (TTC→TTG) |
narI → |
nitrate reductase 1, gamma (cytochrome b(NR)) subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 837,728 | 0 | C | G | 22.4%
| 127.6
/ 34.6
| 67 | F67L (TTC→TTG) | narI | nitrate reductase 1, gamma (cytochrome b(NR)) subunit |
| Reads supporting (aligned to +/- strand): ref base C (27/25); new base G (3/12); total (30/37) |
| Fisher's exact test for biased strand distribution p-value = 3.94e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.68e-01 |
TCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAACAGAAAATGGCA > minE/837659‑837797
|
tCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCActtct < 1:2740018/71‑1 (MQ=255)
tCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCActtct > 1:5613210/1‑71 (MQ=255)
gCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCActtctt < 1:4692638/70‑1 (MQ=255)
aaaGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCgg < 1:1799919/71‑1 (MQ=255)
aGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTa > 1:633968/1‑71 (MQ=255)
gggATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCg > 1:4080490/1‑67 (MQ=255)
gggATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCg > 1:1547980/1‑67 (MQ=255)
gATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTa > 1:1127883/1‑68 (MQ=255)
gAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGa > 1:4804580/1‑71 (MQ=255)
ccTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACttcttc < 1:5253222/58‑1 (MQ=255)
cTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGAcgcc < 1:1498757/71‑1 (MQ=255)
tGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGAcgccg > 1:1827984/1‑71 (MQ=255)
tCGAATCTGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACTg < 1:5667574/71‑1 (MQ=255)
gAATCTGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACTGGa > 1:1772263/1‑71 (MQ=255)
aatcTGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACTGGAt > 1:4149972/4‑71 (MQ=255)
atcTGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACt < 1:4370513/64‑1 (MQ=255)
atcTGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACTGGATg < 1:3530681/69‑1 (MQ=255)
atcTGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACTGGATg < 1:4836129/69‑1 (MQ=255)
aCCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTa < 1:4547925/51‑1 (MQ=255)
aCCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTa < 1:3078725/51‑1 (MQ=255)
tGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTAt > 1:3813579/1‑71 (MQ=255)
tGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTAt > 1:3413289/1‑71 (MQ=255)
gTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGt < 1:1693949/68‑1 (MQ=255)
ttCCATATCGGGATTCTGGGGATTTTTGTCGGTCActtctt > 1:2709699/1‑41 (MQ=255)
ttCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCgg < 1:3601887/44‑1 (MQ=255)
ttCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCgg < 1:2088660/44‑1 (MQ=255)
ttCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCAt < 1:1660383/47‑1 (MQ=16)
ttCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCAt < 1:4474413/47‑1 (MQ=16)
ccATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATgt > 1:453948/1‑46 (MQ=255)
atatCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACCCCGCACTGGATg < 1:1901880/62‑1 (MQ=255)
tatCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCt < 1:1612111/45‑1 (MQ=255)
tatCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCt < 1:625380/45‑1 (MQ=255)
tatCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGcc < 1:2106917/70‑1 (MQ=255)
tatCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCgg < 1:2237207/39‑1 (MQ=16)
tatCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATgtt < 1:1282650/45‑3 (MQ=255)
tatCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATgtt < 1:4838486/45‑3 (MQ=255)
tatCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATgtt < 1:2480542/45‑3 (MQ=255)
cGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGc > 1:4708655/1‑71 (MQ=255)
aTTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGt < 1:3749098/55‑1 (MQ=255)
aTTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGcc < 1:3701736/71‑1 (MQ=255)
ttCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCt < 1:208765/37‑1 (MQ=255)
ttCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCt < 1:3504586/37‑1 (MQ=255)
ttCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCt < 1:5320668/37‑1 (MQ=255)
ttCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGcc < 1:4949025/70‑1 (MQ=255)
cTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTg > 1:2619851/1‑47 (MQ=255)
cTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGAt > 1:974300/1‑71 (MQ=255)
cTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGAt > 1:365107/1‑71 (MQ=255)
cTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGACGCACTGGATGTATGAAGCCTGGCTGCCGAt > 1:5258217/1‑71 (MQ=255)
gggATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTg < 1:878421/70‑1 (MQ=255)
gggATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGa < 1:3201461/71‑1 (MQ=255)
ggATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTAt < 1:15432/50‑1 (MQ=255)
gATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAg > 1:3198810/1‑71 (MQ=255)
aTTTTTGTCGGTCACTTCTTCGGTATGCTGAcgcc > 1:3579565/1‑35 (MQ=255)
aTTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTg > 1:3820107/1‑41 (MQ=255)
aTTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTg > 1:4697662/1‑41 (MQ=255)
aTTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGt < 1:488473/71‑1 (MQ=255)
ttttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTg < 1:4550046/39‑1 (MQ=255)
ttttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTg < 1:2713587/39‑1 (MQ=255)
ttttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTg < 1:4893634/39‑1 (MQ=255)
ttttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAg > 1:174615/1‑68 (MQ=255)
ttttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGt > 1:3932177/1‑69 (MQ=255)
ttttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTg < 1:3362383/70‑1 (MQ=255)
ttttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTg > 1:24118/1‑70 (MQ=255)
cGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGa > 1:3958079/1‑56 (MQ=255)
cGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGa > 1:1508084/1‑56 (MQ=255)
cGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGa > 1:5669370/1‑56 (MQ=255)
ggTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTg > 1:3190265/1‑47 (MQ=255)
ggTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAACAGa > 1:2060130/1‑70 (MQ=255)
ggTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAACAGa > 1:5684658/1‑70 (MQ=255)
ggTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAACAGa > 1:3720324/1‑70 (MQ=255)
tCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAACATaaaa < 1:2201898/71‑1 (MQ=255)
aCTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGAtt < 1:5530285/53‑1 (MQ=255)
ttcttcGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAACAGaaaa < 1:3202934/67‑1 (MQ=255)
cttcGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAACAGAAAATGGCa < 1:868563/70‑1 (MQ=255)
|
TCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAACAGAAAATGGCA > minE/837659‑837797
|
| 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
