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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,433,207 |
T→C |
35.3% |
P75P (CCT→CCC) |
rhlB → |
ATP‑dependent RNA helicase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,433,207 | 0 | T | C | 35.3%
| 30.0
/ 25.7
| 48 | P75P (CCT→CCC) | rhlB | ATP‑dependent RNA helicase |
| Reads supporting (aligned to +/- strand): ref base T (19/12); new base C (3/14); total (22/26) |
| Fisher's exact test for biased strand distribution p-value = 5.91e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.46e-01 |
GCAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTGCCTTAATTATGGCACCGA > minE/2433141‑2433259
|
gcAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCt > 1:622907/1‑67 (MQ=255)
gcAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCt > 1:276339/1‑67 (MQ=255)
gcAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCt > 1:1023716/1‑67 (MQ=255)
gcAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCt > 1:2186343/1‑67 (MQ=255)
gcAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCt > 1:1704563/1‑67 (MQ=255)
cAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCg < 1:344283/69‑1 (MQ=255)
cAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCg < 1:3276465/69‑1 (MQ=255)
cAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCg < 1:1433404/69‑1 (MQ=255)
cAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCg < 1:2979067/69‑1 (MQ=255)
cAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCg < 1:1757181/69‑1 (MQ=255)
aCCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGAtt > 1:475923/1‑69 (MQ=255)
aCCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGAtt > 1:3244702/1‑69 (MQ=255)
aCCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGAtt > 1:533477/1‑69 (MQ=255)
aCCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGAtt > 1:1448/1‑69 (MQ=255)
ccGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTg < 1:2075361/69‑1 (MQ=255)
ccGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTg < 1:1478068/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:1828401/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:1170726/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:3427634/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:1173624/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:3108427/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:2894939/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:2879094/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:2583562/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:2527327/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:68510/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:201827/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:2561370/69‑1 (MQ=255)
gTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:218463/69‑1 (MQ=255)
gggAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg < 1:1484278/64‑1 (MQ=255)
aaaaCGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAg > 1:2073719/1‑69 (MQ=255)
aTGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGa > 1:1224142/1‑67 (MQ=255)
aTGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGa > 1:1621510/1‑67 (MQ=255)
aTGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGa > 1:1466383/1‑67 (MQ=255)
aTGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGa > 1:51639/1‑67 (MQ=255)
aTGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGa > 1:1914318/1‑67 (MQ=255)
cGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCg > 1:391872/1‑51 (MQ=255)
cGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCGATCGCaa > 1:824684/1‑58 (MQ=255)
cGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCCGCGATTGCCGATCGCaa > 1:3311757/1‑58 (MQ=255)
tttCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGcc > 1:667538/1‑68 (MQ=255)
tCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCaa > 1:2407695/1‑54 (MQ=255)
tCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCcgcg > 1:2685765/1‑69 (MQ=255)
tCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCcgcg > 1:2109760/1‑69 (MQ=255)
tACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTg < 1:3337112/68‑1 (MQ=255)
tACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTg < 1:168532/68‑1 (MQ=255)
tACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTg < 1:878589/68‑1 (MQ=255)
aCGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTg < 1:306982/67‑1 (MQ=255)
aCGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTg < 1:996370/67‑1 (MQ=255)
aTCTTCTCTCTCCTCCTGCGATTGCCGCTCGCAAGGTGAATCAGCCGCGTGCCTTAATTATGGCAcc > 1:683857/1‑67 (MQ=255)
aTCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTGCCTTAATTATGGCACCGa > 1:551738/1‑69 (MQ=255)
aTCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTGCCTTAATTATGGCACCGa > 1:555711/1‑69 (MQ=255)
aTCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTGCCTTAATTATGGCACCGa > 1:2799869/1‑69 (MQ=255)
aTCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTGCCTTAATTATGGCACCGa > 1:1201827/1‑69 (MQ=255)
|
GCAAACCGGTACCGGGAAAACGATGGCGTTTCTTACGTCAACGTTTCATTATCTTCTCTCTCATCCTGCGATTGCCGATCGCAAGGTGAATCAGCCGCGTGCCTTAATTATGGCACCGA > minE/2433141‑2433259
|
| 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
