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 |
1,403,231 |
G→A |
42.8% |
P358P (CCG→CCA) |
rtn → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,403,231 | 0 | G | A | 42.8%
| 13.4
/ 33.6
| 49 | P358P (CCG→CCA) | rtn | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (26/2); new base A (9/12); total (35/14) |
| Fisher's exact test for biased strand distribution p-value = 2.33e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
GCCCGCGATGCCGCAGAATTAGAAAAAGTGCTGCCGGTAGGCGTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTGCCCGCA > minE/1403163‑1403294
|
gcgcgcgATGCCGCAGAATTAGAAAAAGTGCTGCCGGTAGGCGTCAAATTTGGTATTAACATTGCGCCg > 1:1460999/4‑69 (MQ=255)
gCCCGCGATGCCGCAGAATTAGAAAAAGTGCTGCCGGTAGGCGTCAAATTTGGTATTAACATTGCGCCg > 1:13621/1‑69 (MQ=255)
gCCCGCGATGCCGCAGAATTAGAAAAAGTGCTGCCGGTAGGCGTCAAATTTGGTATTAACATTGCGCCg > 1:3142835/1‑69 (MQ=255)
gCCCGCGATGCCGCAGAATTAGAAAAAGTGCTGCCGGTAGGCGTCAAATTTGGTATTAACATTGCGCCg > 1:1794918/1‑69 (MQ=255)
gCCCGCGATGCCGCAGAATTAGAAAAAGTGCTGCCGGTAGGCGTCAAATTTGGTATTAACATTGCGCCg > 1:679725/1‑69 (MQ=255)
gcgATGCCGCAGAATTAGAAAAAGTGCTGCCGGTAGGCGTCAAATTTGGTATTAACATTGCGCCGGAcc < 1:3073422/69‑1 (MQ=255)
cgATGCCGCAGATTTAGAAAAAGTGCTGCCGGTAGGCGTCAAATTTGGTATTAACATTGCGCCGGAcc < 1:3043012/68‑1 (MQ=255)
aaTTAGAAAAAGTACTGCCGGTAGGCGTCAAATTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCg < 1:1377287/69‑1 (MQ=255)
aaTTAGAAAAAGTACTGCCGGTAGGCGTCAAATTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCg < 1:3341182/69‑1 (MQ=255)
tAGGCGTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGata > 1:2893130/1‑66 (MQ=255)
tAGGCGTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGata > 1:2114244/1‑66 (MQ=255)
tAGGCGTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGata > 1:584142/1‑66 (MQ=255)
aGGCGTCAAATTTGGTATTAAGATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATcc > 1:2294002/1‑68 (MQ=255)
aGGCGTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATcc > 1:3212364/1‑68 (MQ=255)
aGGCGTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATcc > 1:2297790/1‑68 (MQ=255)
aGGCGTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATcc > 1:2782946/1‑68 (MQ=255)
gTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGaaa > 1:1796584/1‑69 (MQ=255)
gTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGaaa > 1:3193555/1‑69 (MQ=255)
gTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGaaa > 1:3369020/1‑69 (MQ=255)
cAAATTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAG‑AGATATCCAGAAACTg < 1:1474096/69‑1 (MQ=255)
aaaTTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTg < 1:3287216/69‑1 (MQ=255)
aaaTTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTg < 1:2755300/69‑1 (MQ=255)
aaaTTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTg < 1:430281/69‑1 (MQ=255)
aaaTTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTg < 1:1891949/69‑1 (MQ=255)
aaaTTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTg < 1:1875353/69‑1 (MQ=255)
aaTTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTg < 1:1924519/68‑1 (MQ=255)
aaTTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTg < 1:2808129/68‑1 (MQ=255)
aaTTTGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTg < 1:13799/68‑1 (MQ=255)
ttGGCATTAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTg < 1:841413/65‑1 (MQ=255)
tAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTGCTCACTTccc > 1:2273725/1‑68 (MQ=255)
tAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTGCTCACTTCCCt > 1:2196782/1‑69 (MQ=255)
tAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTGCTCACTTCCCt > 1:3348648/1‑69 (MQ=255)
tAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTGCTCACTTCCCt > 1:2410533/1‑69 (MQ=255)
tAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTGCTCACTTCCCt > 1:2221960/1‑69 (MQ=255)
tAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTGCTCACTTCCCt > 1:813402/1‑69 (MQ=255)
tAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTGCTCACTTCCCt > 1:1399758/1‑69 (MQ=255)
tAACATTGCGCCAGCCCACTTGCACAGCGAAAGCTTTAAAGCGGATATCCAGAAACTGCTCACTTCCCt > 1:86670/1‑69 (MQ=255)
tAACATTGCGCCAGCCCACTTGCACAGCGAAAGCATTAAAGCGGaaat > 1:2885354/1‑48 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAGAGCTTTAAAGCAGATATCCAGa > 1:1358038/1‑52 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGa > 1:3236588/1‑52 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGa > 1:2478745/1‑52 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGa > 1:2643961/1‑52 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCt > 1:1358902/1‑68 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTg > 1:1069973/1‑69 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTg > 1:2210302/1‑69 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTg > 1:626870/1‑69 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTg > 1:1411727/1‑69 (MQ=255)
aaCATTGCGCCGGACCATCTGCACAGCGAAAGCTATAAAGCAGATATCCAGa > 1:3247264/1‑52 (MQ=255)
aaCATTGCGCCGGACCATCTGAACAGCGAAAGCTTTAAAGCAGATATcc > 1:2636501/1‑49 (MQ=255)
gcgcCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGACACTGCTCACTTCCCTGCCCGc > 1:1085938/1‑68 (MQ=255)
gcgcCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTGCCCGca > 1:2156103/1‑69 (MQ=255)
gcgcCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTGCCCGca > 1:1987304/1‑69 (MQ=255)
gcgcCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTGCCCGca > 1:1931908/1‑69 (MQ=255)
gcgcCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTGCCCGc > 1:2940371/1‑68 (MQ=255)
|
GCCCGCGATGCCGCAGAATTAGAAAAAGTGCTGCCGGTAGGCGTCAAATTTGGTATTAACATTGCGCCGGACCATCTGCACAGCGAAAGCTTTAAAGCAGATATCCAGAAACTGCTCACTTCCCTGCCCGCA > minE/1403163‑1403294
|
| 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
