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 |
912,291 |
C→T |
26.1% |
I135I (ATC→ATT) |
ompG → |
outer membrane porin |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 912,291 | 0 | C | T | 26.1%
| 98.9
/ 30.5
| 84 | I135I (ATC→ATT) | ompG | outer membrane porin |
| Reads supporting (aligned to +/- strand): ref base C (52/10); new base T (5/17); total (57/27) |
| Fisher's exact test for biased strand distribution p-value = 3.97e-07 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.10e-01 |
TATGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGTATA > minE/912229‑912355
|
tATGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCa < 1:2681922/69‑1 (MQ=255)
tATGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCa < 1:1539364/69‑1 (MQ=255)
tATGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCa < 1:1538572/69‑1 (MQ=255)
aTGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAg > 1:1101985/1‑69 (MQ=255)
aTGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAg > 1:399341/1‑69 (MQ=255)
aTGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAg > 1:2589741/1‑69 (MQ=255)
aTGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAg > 1:2119305/1‑69 (MQ=255)
aTGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAg > 1:148038/1‑69 (MQ=255)
aTGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAg > 1:3163933/1‑69 (MQ=255)
tATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTgg < 1:718785/69‑1 (MQ=255)
tATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTgg < 1:1106013/69‑1 (MQ=255)
aCGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATcg > 1:2246603/1‑51 (MQ=255)
aCGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGAc > 1:1719284/1‑59 (MQ=255)
aCGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGa > 1:2426843/1‑69 (MQ=255)
aCGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGa > 1:2382940/1‑69 (MQ=255)
aCGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGa < 1:1687458/69‑1 (MQ=255)
tgatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAact < 1:2748826/69‑1 (MQ=255)
tgatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAact < 1:1385058/69‑1 (MQ=255)
tgatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAact < 1:297724/69‑1 (MQ=255)
tgatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAact < 1:3420081/69‑1 (MQ=255)
tgatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAact < 1:112337/69‑1 (MQ=255)
tgatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAact < 1:1948555/69‑1 (MQ=255)
tgatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAact < 1:2071753/69‑1 (MQ=255)
gatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAact < 1:2219713/68‑1 (MQ=255)
gatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCa < 1:261429/51‑1 (MQ=255)
gatgaACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAactg > 1:3322917/1‑69 (MQ=255)
gggTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGa < 1:2697523/56‑1 (MQ=255)
ggTAAAGACACGGCGAATATGCAGCGCTGGAGAATCGCGCCAGACTGGGATGTGAAACTGACTGACGa > 1:3231390/1‑68 (MQ=255)
ggTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAACTGACTGACGAt < 1:3136383/69‑1 (MQ=255)
ggTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAACTGACTGACGAt < 1:1023120/69‑1 (MQ=255)
ggTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAACTGACTGACGAt < 1:534993/69‑1 (MQ=255)
ggTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAACTGACTGACGAt < 1:2050991/69‑1 (MQ=255)
ggTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAACTGACTGACGAt < 1:1995393/69‑1 (MQ=255)
ggTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAACTGACTGACGAt < 1:569441/69‑1 (MQ=255)
ggTAAAGACACGGCGAATATGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAACTGACTGACGAt < 1:960099/69‑1 (MQ=255)
gACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACg < 1:2620049/68‑1 (MQ=255)
gACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACg < 1:1745796/68‑1 (MQ=255)
gACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:2037019/1‑69 (MQ=255)
gACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:476031/1‑69 (MQ=255)
gACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:189417/1‑69 (MQ=255)
gACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:2979651/1‑69 (MQ=255)
gACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:1200115/1‑69 (MQ=255)
gACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:2405664/1‑69 (MQ=255)
gACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:3182049/1‑69 (MQ=255)
gACAAGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:2874629/1‑69 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGAtgt > 1:1797115/1‑46 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:3011699/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:3259121/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:534637/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:563881/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:583719/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:760563/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:992166/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:2692208/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:1184428/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:2193707/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:2557823/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:1796761/1‑68 (MQ=255)
acacGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:1348118/1‑68 (MQ=255)
acacGGCGAATATGCAGCGATGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGt > 1:1148115/1‑68 (MQ=255)
tGCAGCGCTGGAAAATTGCGCCAGACTGGGATGTGAAACTGACTGACGAt < 1:2057963/50‑1 (MQ=255)
cAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGgttggttg > 1:2392527/1‑69 (MQ=255)
cAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGgttggttg > 1:1246345/1‑69 (MQ=255)
cAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGgttggttg > 1:2872350/1‑69 (MQ=255)
cAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGgttggttg > 1:672463/1‑69 (MQ=255)
cAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGgttggttg > 1:1661381/1‑69 (MQ=255)
cAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGgttggttg > 1:2560722/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:694061/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:1102435/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:430423/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:739591/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:1682577/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:1658142/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:550722/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:1245597/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:370262/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:2353575/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:1225942/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:3315876/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:2425510/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:2439154/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtata > 1:1472368/1‑69 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGtat > 1:3037410/1‑68 (MQ=255)
aaaTCGCGCCAGACTGGGATGTGAAAATGACTGACGATTTACGTTTCAAc > 1:219288/1‑50 (MQ=255)
aaTTGCGCCAGACTGGGATGTGAAACTGACTGACGAt < 1:551419/37‑1 (MQ=255)
|
TATGGTTATCACTACGTTGATGAACCGGGTAAAGACACGGCGAATATGCAGCGCTGGAAAATCGCGCCAGACTGGGATGTGAAACTGACTGACGATTTACGTTTCAACGGTTGGTTGTCGATGTATA > minE/912229‑912355
|
| 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
