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 |
309,827 |
C→A |
29.4% |
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 | 29.4%
| 159.8
/ 51.6
| 85 | V1016L (GTA→TTA) ‡ | acrB | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base C (24/35); new base A (11/14); total (35/50) |
| Fisher's exact test for biased strand distribution p-value = 8.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTA > minE/309759‑309897
|
ttCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCg > 1:3118460/1‑71 (MQ=255)
tCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGt > 1:3062001/1‑71 (MQ=255)
cATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGtt > 1:726645/1‑71 (MQ=255)
aTTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGtt < 1:5632875/70‑1 (MQ=255)
aTTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGtt < 1:5639346/70‑1 (MQ=255)
gCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGt < 1:4802089/69‑1 (MQ=255)
gCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGt < 1:1037312/69‑1 (MQ=255)
ttAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt > 1:1446701/2‑71 (MQ=16)
ttAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt > 1:221571/2‑71 (MQ=16)
cTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCg < 1:5569396/58‑1 (MQ=255)
tAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCg < 1:3829365/57‑1 (MQ=255)
tAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTg < 1:1550459/60‑1 (MQ=255)
tAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt < 1:701302/70‑1 (MQ=255)
tAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt < 1:1254904/70‑1 (MQ=255)
tAAAGCAACGGCGGATCACCACAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCAt < 1:2154671/70‑1 (MQ=255)
aaaGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATcc > 1:3255651/1‑71 (MQ=255)
aaGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATc < 1:3234260/69‑1 (MQ=255)
aaGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATc < 1:3879147/69‑1 (MQ=255)
aaGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATc < 1:2545637/69‑1 (MQ=255)
aGCGGCGGCGAACCAACACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCg > 1:3422099/1‑71 (MQ=255)
cggcggcgAACCACCACAAAGAATACCGGAACGAAGAAGATT‑CCAGTACCGTTGCGGTCACCATcc > 1:4777737/1‑66 (MQ=255)
ggcggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGcc < 1:3265306/70‑1 (MQ=255)
cggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGc < 1:4354259/53‑1 (MQ=255)
cggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGc < 1:2851986/53‑1 (MQ=255)
cggcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGc < 1:3891948/53‑1 (MQ=255)
gcgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTAGCg < 1:1792654/47‑1 (MQ=255)
cgAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTa < 1:4164197/70‑1 (MQ=255)
aaCCACCACAAAGAATA‑CGGAACGAAGAAGATTGCCAGTAc > 1:3598405/1‑41 (MQ=38)
accaccACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACAcc > 1:4442604/1‑71 (MQ=255)
tcaccacAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTAcccc > 1:314986/2‑70 (MQ=255)
ccaccaCAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCa > 1:5409611/1‑63 (MQ=255)
accacAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGcc < 1:3281504/59‑1 (MQ=255)
accacAAAGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTaccc > 1:5354213/1‑65 (MQ=16)
cacaAAGAATACCGGAACGAAGAAGATTGCCAGTAc > 1:532980/1‑36 (MQ=255)
cacaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGcc < 1:1440765/57‑1 (MQ=255)
cacaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCa > 1:4718558/1‑59 (MQ=255)
cacaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAc > 1:4126667/1‑71 (MQ=255)
acaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACCCCGGTAcc > 1:5554540/1‑71 (MQ=255)
caAAGAATACCGGAACTAAGAAGATTGCCAGTACCGTTGCGGTCAc < 1:1065477/46‑1 (MQ=255)
caAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTTCGGTCAc < 1:4336929/46‑1 (MQ=255)
caAAGAATACCGGAACCAAGAAGATTGCCAGGACCGTTGCGGCCAc < 1:5163425/46‑1 (MQ=255)
aaGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa > 1:5162098/1‑70 (MQ=255)
aaGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATAccca > 1:849491/1‑68 (MQ=12)
aGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAcc < 1:847248/67‑1 (MQ=255)
aGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAcc < 1:625993/67‑1 (MQ=255)
aGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAcc < 1:182003/67‑1 (MQ=255)
aGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATtcctcc < 1:973145/52‑1 (MQ=12)
aGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATtcctcc < 1:31127/52‑1 (MQ=12)
gAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCAcag > 1:2923753/1‑69 (MQ=255)
acaCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCg > 1:3298615/3‑71 (MQ=255)
acaCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCg > 1:4712527/3‑71 (MQ=255)
tACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa > 1:5670355/1‑65 (MQ=255)
tACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa > 1:2475731/1‑65 (MQ=255)
aCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt < 1:5275557/71‑1 (MQ=255)
ccGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTac < 1:878289/52‑1 (MQ=255)
cGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATAccca > 1:5372972/1‑60 (MQ=255)
ggAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTac < 1:5521459/50‑1 (MQ=255)
ggAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTg > 1:309971/1‑71 (MQ=255)
ggAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTg < 1:2365160/71‑1 (MQ=255)
gtaCGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgc < 1:2736173/69‑1 (MQ=255)
gtaCGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgc < 1:2910880/69‑1 (MQ=255)
gAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgc < 1:2729606/71‑1 (MQ=255)
aaCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTacac > 1:3542944/1‑50 (MQ=255)
aaCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTacac > 1:5452146/1‑50 (MQ=255)
aCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgc > 1:2623255/1‑71 (MQ=255)
cGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgcg > 1:2352911/1‑71 (MQ=255)
cGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt > 1:487488/1‑64 (MQ=255)
cGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt > 1:1336105/1‑64 (MQ=255)
gaagaaGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCAt < 1:5150395/42‑1 (MQ=255)
gaagaaGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgcgc < 1:4858816/71‑1 (MQ=255)
gaagaaGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgcgcgc < 1:1760126/71‑1 (MQ=12)
aagaagATTGCCAGTACCGTTGCGGTCACCATCCCGCCCAt < 1:3118294/41‑1 (MQ=255)
aagaagATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt < 1:4603109/62‑1 (MQ=255)
aagaagATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt < 1:2606199/62‑1 (MQ=255)
aagaagATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt < 1:1588986/62‑1 (MQ=255)
gaagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCgg < 1:1306413/71‑1 (MQ=255)
gaagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCgg < 1:1517037/71‑1 (MQ=255)
aagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCATTCTTCGCGCCGGa < 1:448472/71‑1 (MQ=255)
gaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAAc < 1:91297/71‑1 (MQ=255)
gaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAAc > 1:3420077/1‑71 (MQ=255)
gaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAAc > 1:3216696/1‑71 (MQ=255)
aTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAAc < 1:2801117/70‑1 (MQ=255)
aTTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgcgcg < 1:4018313/63‑1 (MQ=255)
aTTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgcgcg < 1:4069408/63‑1 (MQ=255)
gCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAg > 1:4999943/1‑70 (MQ=255)
tACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAg > 1:1582566/1‑71 (MQ=255)
aCCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAg > 1:5516986/1‑70 (MQ=255)
ccGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTa > 1:2665121/1‑71 (MQ=255)
|
TTCATTCTTGCGGCTAAAGCGGCGGCGAACCACCACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTA > minE/309759‑309897
|
| 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
