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 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
309,827 |
C→A |
18.8% |
V1016L (GTA→TTA) ‡ |
acrB ← |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 309,827 | 0 | C | A | 18.8%
| 197.6
/ 22.2
| 74 | V1016L (GTA→TTA) ‡ | acrB | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base C (34/26); new base A (9/5); total (43/31) |
| Fisher's exact test for biased strand distribution p-value = 7.66e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
TCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAG > minE/309760‑309895
|
tCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGt > 1:2942161/1‑71 (MQ=255)
tCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGt > 1:2778805/1‑71 (MQ=255)
tCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGt > 1:725538/1‑71 (MQ=255)
cATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCg < 1:3114024/69‑1 (MQ=255)
cATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGtt > 1:859975/1‑71 (MQ=255)
aTTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGtt < 1:3180454/70‑1 (MQ=255)
aTTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTg > 1:3272525/1‑71 (MQ=255)
aTTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTg > 1:2099800/1‑71 (MQ=255)
cTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCgg > 1:3006742/1‑71 (MQ=255)
gCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCa > 1:1647239/1‑71 (MQ=255)
tAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCa > 1:2418527/1‑66 (MQ=255)
tAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt < 1:1489815/70‑1 (MQ=255)
aaGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATcc < 1:749825/70‑1 (MQ=255)
aGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCg > 1:1225334/1‑71 (MQ=255)
aGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCg > 1:3948018/1‑71 (MQ=255)
cggcggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGcc > 1:1194655/1‑71 (MQ=255)
caacggcggATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATtcctcc > 1:2110854/4‑71 (MQ=255)
cggcggATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATtcct > 1:1561204/1‑65 (MQ=255)
ggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCAtt < 1:1048865/71‑1 (MQ=255)
ggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCAt > 1:1330923/1‑70 (MQ=255)
gcgAACCACCACAAAGACTACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa < 1:2209098/71‑1 (MQ=255)
gcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa < 1:3528139/71‑1 (MQ=255)
gcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa < 1:1784113/71‑1 (MQ=255)
gcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa < 1:3590208/71‑1 (MQ=255)
gcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa < 1:2805596/71‑1 (MQ=255)
cgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCg < 1:457684/46‑1 (MQ=255)
cgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa > 1:2941047/1‑70 (MQ=255)
gAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTaca < 1:324198/71‑1 (MQ=255)
accaccACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCa > 1:1844696/1‑55 (MQ=255)
accaccACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCa > 1:2423986/1‑55 (MQ=255)
accaccACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCa > 1:3942667/1‑55 (MQ=255)
ccaccaCAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATccc > 1:2098850/1‑58 (MQ=255)
ccaccaCAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCg > 1:834336/1‑71 (MQ=255)
ccacAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa < 1:2752933/63‑1 (MQ=255)
ccacAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa < 1:460194/63‑1 (MQ=255)
cacaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAc > 1:968756/1‑71 (MQ=255)
acaAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAttc > 1:366737/1‑50 (MQ=16)
acaAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATAcc > 1:3566960/1‑71 (MQ=255)
caAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGccc < 1:3565250/56‑1 (MQ=255)
aaaGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa > 1:1611431/1‑71 (MQ=255)
aaaGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGcag > 1:3773625/1‑39 (MQ=19)
aaaGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAtt > 1:1296639/1‑48 (MQ=16)
aGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATAccca > 1:185324/1‑67 (MQ=255)
gAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTg > 1:1474655/1‑71 (MQ=255)
acaCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCg < 1:3082222/69‑1 (MQ=255)
aTACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCg < 1:350623/71‑1 (MQ=255)
aCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt < 1:1227198/71‑1 (MQ=255)
ccGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTc < 1:5099/71‑1 (MQ=255)
ccGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGtt < 1:912952/70‑1 (MQ=255)
cGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCt < 1:756989/71‑1 (MQ=255)
gAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgc > 1:3107272/1‑71 (MQ=255)
taCGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgcg > 1:350509/2‑71 (MQ=255)
aCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgc < 1:3699715/71‑1 (MQ=255)
aCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgc < 1:3761026/71‑1 (MQ=255)
aCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgc > 1:1502455/1‑71 (MQ=255)
aCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcg > 1:2198179/1‑70 (MQ=255)
aCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGGTCTgcgc < 1:1468783/71‑1 (MQ=255)
cGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgcg < 1:2391592/71‑1 (MQ=255)
gacgaagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgcgc < 1:3693684/68‑1 (MQ=255)
gaagaaGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgcgc < 1:844117/71‑1 (MQ=255)
gaagaaGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgcgcgc > 1:2518292/1‑71 (MQ=255)
gaagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCgg < 1:1516309/71‑1 (MQ=255)
gaagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCg > 1:432992/1‑70 (MQ=255)
aagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCgg > 1:343039/1‑70 (MQ=255)
aagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCgg > 1:1533154/1‑70 (MQ=255)
gaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAAc < 1:1058779/71‑1 (MQ=255)
ttGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCa < 1:1277295/71‑1 (MQ=255)
tGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAg > 1:2240384/1‑71 (MQ=255)
gTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCAc > 1:3017790/1‑69 (MQ=255)
gTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCAc > 1:2411339/1‑69 (MQ=255)
tACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGcc > 1:3569415/1‑57 (MQ=255)
tACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGcc > 1:2374236/1‑57 (MQ=255)
aCCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCa > 1:467581/1‑69 (MQ=255)
aCCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAg < 1:447574/70‑1 (MQ=255)
|
TCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAG > minE/309760‑309895
|
| 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
