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 |
395,912 |
C→T |
46.5% |
G421G (GGC→GGT) |
ahpF → |
alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 395,912 | 0 | C | T | 46.5%
| 13.1
/ 72.8
| 88 | G421G (GGC→GGT) | ahpF | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| Reads supporting (aligned to +/- strand): ref base C (27/20); new base T (24/17); total (51/37) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
ACGTCGACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAGCGGCGATATTCACAACATCG > minE/395863‑395970
|
aCGTCGACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTgg < 1:34085/69‑1 (MQ=255)
aCGTCGACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTgg < 1:292407/69‑1 (MQ=255)
aCGTCGACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTgg < 1:1216574/69‑1 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:157335/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:2329571/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:1765000/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:1787063/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:2158087/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:2459522/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:263725/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:3136478/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:3252835/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:391265/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:5333/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:587102/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:66765/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:883279/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:981766/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:1411579/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:1525377/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:1354717/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:1331847/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAatat > 1:1138839/1‑69 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAata > 1:1611394/1‑68 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAata > 1:974442/1‑68 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGCAAAGTCGTAGGTCTGGAata > 1:3418258/1‑68 (MQ=255)
gACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGTAGAAAAGTCGTAGGTCTGGAata > 1:2933372/1‑68 (MQ=255)
attattCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAata > 1:502304/1‑65 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGt > 1:1037742/1‑47 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTc > 1:1541734/1‑48 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTc > 1:2598743/1‑48 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTc > 1:271767/1‑48 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTc > 1:1948765/1‑48 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTc > 1:1914177/1‑48 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTc > 1:703206/1‑48 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTc > 1:1046292/1‑48 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTc > 1:1719412/1‑48 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTc > 1:1647888/1‑48 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGAt > 1:3061261/1‑69 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGAt > 1:3431500/1‑69 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGAt > 1:1548073/1‑69 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGAt > 1:2396844/1‑69 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGAt > 1:2213818/1‑69 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGAt > 1:1882467/1‑69 (MQ=255)
attCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGAt > 1:1413265/1‑69 (MQ=255)
cTGAATGCGCAAACCACGGAAGTTAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCgt > 1:2774064/1‑69 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:3301498/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:1609992/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:973594/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:1075854/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:1088294/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:420963/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:1906617/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:1924881/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:2005845/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:1020793/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:2650340/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:27271/40‑1 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAgcg > 1:1431552/1‑69 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAgcg > 1:298342/1‑69 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAgcg > 1:3135382/1‑69 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAgcg > 1:5787/1‑69 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAgcg > 1:2300311/1‑69 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAgc > 1:813544/1‑68 (MQ=255)
cgcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTAAgcg > 1:3389951/1‑69 (MQ=255)
gcAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGt < 1:3383639/39‑1 (MQ=255)
aaaGGCGACGGCAGCAAAGTCGTTGGTCTGGATTATCGAGATCGTGTCAGCGGCGATATTcac < 1:2133979/63‑1 (MQ=255)
aaaGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAGCGGCGATATTcac < 1:2634941/63‑1 (MQ=255)
aaaGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAGCGGCGATATTcac < 1:1062452/63‑1 (MQ=255)
aaaGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATAGTGTCAGCGGCGATATTCA‑AACATCg > 1:508857/1‑69 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATct < 1:287758/68‑2 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:1110828/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:1758742/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:1493446/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:2130336/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:2075539/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:2295345/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:2406819/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:1873356/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:2180873/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:1103461/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:353815/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:260662/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:3311259/68‑1 (MQ=255)
aGGCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:3340196/68‑1 (MQ=255)
aGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAGCGGCGATATTCACAACATCg < 1:1319405/68‑1 (MQ=255)
ggCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:2688288/67‑1 (MQ=255)
ggCGACGGTAGCAAAGTCGTAGGTCTGGAATATCGCGATCGTGTCAGCGGCAATATTCACAACATCg < 1:2310670/67‑1 (MQ=255)
|
ACGTCGACATTATTCTGAATGCGCAAACCACGGAAGTGAAAGGCGACGGCAGCAAAGTCGTTGGTCTGGAATATCGAGATCGTGTCAGCGGCGATATTCACAACATCG > minE/395863‑395970
|
| 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
