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 |
|
A2 F17 I0 R2
|
278 |
43.2 |
2215644 |
94.6% |
2095999 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,807,377 |
T→C |
6.4% |
intergenic (+58/+6) |
emrB → / ← luxS |
multidrug efflux system protein/S‑ribosylhomocysteinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,807,377 | 0 | T | C | 6.4%
| 160.5
/ 4.0
| 62 | intergenic (+58/+6) | emrB/luxS | multidrug efflux system protein/S‑ribosylhomocysteinase |
| Reads supporting (aligned to +/- strand): ref base T (27/31); new base C (2/2); total (29/33) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01 |
CACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGAT > minE/1807314‑1807442
|
cACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGAc > 1:878929/1‑70 (MQ=255)
cACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGAc > 1:1406649/1‑70 (MQ=255)
aCTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTa > 1:681127/1‑64 (MQ=255)
cTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGAc > 1:1721617/1‑68 (MQ=255)
aattACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGa < 1:238389/67‑1 (MQ=255)
aGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGa < 1:1463810/69‑1 (MQ=255)
gTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTa > 1:1524576/1‑59 (MQ=255)
aCAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGAtgtg > 1:278180/1‑70 (MQ=255)
aCAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGAtg > 1:318135/1‑68 (MQ=255)
aaGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTAc > 1:99019/1‑52 (MQ=255)
aaGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTcc > 1:670367/1‑71 (MQ=255)
aGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCa > 1:1251888/1‑65 (MQ=255)
ccAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGc < 1:1347257/71‑1 (MQ=255)
acAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGt < 1:1054118/64‑1 (MQ=255)
gTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAAc < 1:1314936/71‑1 (MQ=255)
gTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAAc < 1:1267563/71‑1 (MQ=255)
tCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGAc < 1:1361459/48‑1 (MQ=255)
cATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTtc > 1:1614294/1‑71 (MQ=255)
cATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTtc > 1:2118426/1‑71 (MQ=255)
aTTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGtt < 1:278143/59‑1 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGa > 1:2205516/1‑47 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGa > 1:663549/1‑47 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGACTAGAt > 1:599382/1‑48 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTctct < 1:48841/70‑1 (MQ=255)
cTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTGTTTCgg < 1:1918863/71‑1 (MQ=255)
cTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCgg < 1:1920989/71‑1 (MQ=255)
cTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCgg < 1:859961/71‑1 (MQ=255)
cTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCgg < 1:508361/71‑1 (MQ=255)
tGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCgg > 1:568936/1‑70 (MQ=255)
tGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTCTCttt < 1:914176/67‑1 (MQ=255)
gCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGc < 1:817433/69‑1 (MQ=255)
gCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGc < 1:1965675/69‑1 (MQ=255)
gCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCa > 1:189495/1‑70 (MQ=255)
gCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAg > 1:278501/1‑71 (MQ=255)
ttttCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGc > 1:1136501/1‑70 (MQ=255)
ttttCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGc > 1:1291037/1‑70 (MQ=255)
tCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCtt > 1:443198/1‑57 (MQ=255)
aattaattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCa < 1:364064/67‑1 (MQ=255)
attaattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCtt < 1:1406361/54‑1 (MQ=255)
attaattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCtt < 1:1580237/54‑1 (MQ=255)
attaattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCtt < 1:179381/54‑1 (MQ=255)
ttaattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCgg < 1:2117578/57‑1 (MQ=255)
ttaattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGttctt > 1:1145562/1‑71 (MQ=255)
ttaattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGttctt > 1:530812/1‑71 (MQ=255)
aattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGttcttc < 1:411884/70‑1 (MQ=255)
attGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGttcttc < 1:1992819/69‑1 (MQ=255)
attGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGt > 1:1632488/1‑71 (MQ=255)
ttGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGtt < 1:1321306/71‑1 (MQ=255)
gtgAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTg < 1:687084/70‑1 (MQ=255)
aaGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGt > 1:2186135/1‑71 (MQ=255)
aGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAg > 1:903437/1‑50 (MQ=255)
aGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGtt < 1:1849907/71‑1 (MQ=255)
aGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGtt < 1:1226061/71‑1 (MQ=255)
aGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGtt < 1:494710/71‑1 (MQ=255)
aGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGtt < 1:1020474/71‑1 (MQ=255)
aTAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCATTGCCAGTTCTTCGTTGCTGTTGa > 1:705634/1‑71 (MQ=255)
aTAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGttct < 1:1024157/58‑1 (MQ=255)
aTAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGtt < 1:255325/69‑1 (MQ=255)
tAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGa > 1:540122/1‑70 (MQ=255)
tAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGa > 1:286497/1‑70 (MQ=255)
tAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGAt < 1:227794/71‑1 (MQ=255)
aGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGtt < 1:782413/67‑1 (MQ=255)
ttACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGa > 1:43132/1‑66 (MQ=255)
|
CACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGAT > minE/1807314‑1807442
|
| 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
