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 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,807,377 |
T→C |
26.1% |
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 | 26.1%
| 117.5
/ 47.8
| 69 | intergenic (+58/+6) | emrB/luxS | multidrug efflux system protein/S‑ribosylhomocysteinase |
| Reads supporting (aligned to +/- strand): ref base T (27/24); new base C (14/4); total (41/28) |
| Fisher's exact test for biased strand distribution p-value = 9.43e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGCGCACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGATG > minE/1807310‑1807443
|
tGCGCACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACt < 1:2417971/71‑1 (MQ=255)
tGCGCACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACt < 1:1426814/71‑1 (MQ=255)
tGCGCACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACt < 1:4036045/71‑1 (MQ=255)
gcACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGAc < 1:2208091/71‑1 (MQ=255)
aCTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATACTTTACTGAc < 1:3628271/69‑1 (MQ=255)
cTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGAc > 1:953252/1‑68 (MQ=255)
cTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGAc > 1:2359204/1‑68 (MQ=255)
cTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGAc > 1:1438590/1‑68 (MQ=255)
tAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGAc > 1:3177017/1‑67 (MQ=255)
aGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGAtg > 1:335271/1‑71 (MQ=255)
aGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGAtg > 1:3919249/1‑71 (MQ=255)
tACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTa < 1:2877760/58‑1 (MQ=255)
tACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTa < 1:3348831/58‑1 (MQ=255)
tACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTa < 1:1538395/58‑1 (MQ=255)
tACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTa < 1:3741353/58‑1 (MQ=255)
aCTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGACTAGATGTGCAGt < 1:304204/71‑1 (MQ=255)
aCTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGACTAGATGTGCAGt < 1:566316/71‑1 (MQ=255)
aaGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGttt > 1:672864/1‑50 (MQ=255)
aaGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTa > 1:1768583/1‑51 (MQ=255)
aaGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTcc > 1:1891980/1‑71 (MQ=255)
aGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGACTAGATGTGCAGTTCCt < 1:1050447/71‑1 (MQ=255)
gCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTAc < 1:1816314/50‑1 (MQ=255)
gCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTAc < 1:4168711/50‑1 (MQ=255)
aGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGc < 1:2403578/69‑1 (MQ=255)
gTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGc < 1:2238706/68‑1 (MQ=255)
ttCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTa < 1:2559358/51‑1 (MQ=255)
ttCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTa < 1:2564416/51‑1 (MQ=255)
tCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTa > 1:2336549/1‑43 (MQ=255)
cATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGtt > 1:901791/1‑60 (MQ=255)
cATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTtc > 1:3347854/1‑71 (MQ=255)
ttGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTctct > 1:937685/1‑71 (MQ=255)
ttGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTctct > 1:891820/1‑71 (MQ=255)
ttGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTctct > 1:3377037/1‑71 (MQ=255)
tggaCTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACATCTCtt > 1:1823234/4‑71 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCtt > 1:3569554/1‑71 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCtt > 1:352306/1‑71 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCtt > 1:533842/1‑71 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACATCTCtt > 1:481012/1‑71 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACATCTCtt > 1:140831/1‑71 (MQ=255)
tGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACATCTCtt > 1:350817/1‑71 (MQ=255)
gAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCttt > 1:1137668/1‑71 (MQ=255)
gAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCttt > 1:3232815/1‑71 (MQ=255)
gAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCttt > 1:2378565/1‑71 (MQ=255)
gAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCtt < 1:568194/70‑1 (MQ=255)
cTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCgg < 1:4171504/71‑1 (MQ=255)
cTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCgg < 1:2608529/71‑1 (MQ=255)
cTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCgg < 1:1511890/71‑1 (MQ=255)
tGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAAc < 1:3878751/59‑1 (MQ=255)
gCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGc < 1:2646273/69‑1 (MQ=255)
ttttttCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCttt < 1:3235151/63‑1 (MQ=255)
ttttCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGc > 1:3206830/1‑70 (MQ=255)
ttttCAATTAATTGTGAAGATAGTTCACTGACTAGa > 1:1362336/1‑36 (MQ=255)
ttttCAATTAATTGTGAAGATAGTTCACTGACTAGa > 1:4242613/1‑36 (MQ=255)
tttCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGc > 1:2396589/1‑69 (MQ=255)
tCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGt > 1:953896/1‑71 (MQ=255)
tCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGt > 1:1869143/1‑71 (MQ=255)
aattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCg > 1:632890/1‑71 (MQ=255)
aattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCg > 1:3744648/1‑71 (MQ=255)
aattGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCg > 1:3776916/1‑71 (MQ=255)
aattGTGAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCg > 1:422797/1‑71 (MQ=255)
aattGTGAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCg > 1:369658/1‑71 (MQ=255)
aattGTGAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCg > 1:1388646/1‑71 (MQ=255)
attGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCg < 1:2867478/70‑1 (MQ=255)
attGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCg < 1:572303/70‑1 (MQ=255)
tgtgAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAg > 1:2413794/1‑55 (MQ=255)
tgtgAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAg > 1:3717668/1‑55 (MQ=255)
tgtgAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTg > 1:2745274/1‑71 (MQ=255)
tgtgAAGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTg > 1:2209732/1‑71 (MQ=255)
aaGATAGTTCACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTg < 1:1887948/70‑1 (MQ=255)
aGTTCACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGATg > 1:120235/1‑71 (MQ=255)
|
TGCGCACTAAGTACAACTAAGCCAGTTCATTTGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTAGATGTGCAGTTCCTGCAACTTCTCTTTCGGCAGTGCCAGTTCTTCGTTGCTGTTGATG > minE/1807310‑1807443
|
| 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
