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 |
|
A1 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,800,301 |
A→C |
10.5% |
F119C (TTC→TGC) |
pheS ← |
phenylalanine tRNA synthetase, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,800,301 | 0 | A | C | 10.5%
| 126.3
/ 13.1
| 57 | F119C (TTC→TGC) | pheS | phenylalanine tRNA synthetase, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base A (19/32); new base C (4/2); total (23/34) |
| Fisher's exact test for biased strand distribution p-value = 2.08e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
GCATCGAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTCAATGCGACGAC > W3110S.gb/1800232‑1800364
|
gCATCGAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCgaagaa < 1:2348358/71‑1 (MQ=255)
cATCGAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGaaa > 1:2453857/1‑71 (MQ=255)
aTCGAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCgaaga < 1:3577348/68‑1 (MQ=255)
tCGAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACt < 1:364179/71‑1 (MQ=255)
tCGAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACt > 1:3414212/1‑71 (MQ=255)
gAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACttt > 1:1926380/1‑71 (MQ=255)
gAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACtt < 1:1634696/70‑1 (MQ=255)
gAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCAAGGTAAAGCCAAGCTCACCGAAGAAACttt > 1:49380/1‑71 (MQ=255)
aaGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTc < 1:4115845/71‑1 (MQ=255)
aaGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTc < 1:4499393/71‑1 (MQ=255)
aaGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTc < 1:676104/71‑1 (MQ=255)
gTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGCAACTTTCGa > 1:4334883/1‑71 (MQ=255)
aTGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATa < 1:2287875/70‑1 (MQ=255)
tGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACt < 1:4418985/62‑1 (MQ=255)
tAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGCAACTTTCGATACGGTc > 1:3912586/1‑71 (MQ=255)
tAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACtt > 1:838487/1‑60 (MQ=255)
tAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTc < 1:2747328/71‑1 (MQ=255)
cGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATg > 1:1132132/1‑71 (MQ=255)
gTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGaaa > 1:2258634/1‑52 (MQ=255)
gTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATgg < 1:3727527/71‑1 (MQ=255)
gTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATgg < 1:925510/71‑1 (MQ=255)
tCTTCGATTTCCGGCCCGGTTGCCACGTTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATgg < 1:2738948/70‑1 (MQ=255)
ttCGATTTCCGGCCCGGTTGCGACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGAt < 1:4143938/66‑1 (MQ=255)
ttCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCgaaga < 1:2739846/47‑1 (MQ=255)
ttCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTc < 1:449149/54‑1 (MQ=255)
cGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACgg > 1:1846500/1‑71 (MQ=255)
tttCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCgaagaa < 1:932580/43‑1 (MQ=255)
tttCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTa < 1:1384024/71‑1 (MQ=255)
tttCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTa < 1:3599066/71‑1 (MQ=255)
tCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATa > 1:185011/1‑51 (MQ=255)
cGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACTGGTAACCGGATg > 1:156805/1‑70 (MQ=255)
ggTTGCCACGGTAAAGCCAAGCTCACCGAAGCAACTTTCGATACGGTCGATGGTACGGGTAACCGGATg > 1:1142339/1‑69 (MQ=255)
ggTTGCCACGGTAAAGCCAAGCTCACCGAAGCAACTTTCGATACGGTCGATGATACGGGTAACCGGa < 1:373296/67‑1 (MQ=255)
gTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTc < 1:1514089/38‑1 (MQ=255)
gTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAAc < 1:2301036/62‑1 (MQ=255)
gTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATg > 1:4241357/1‑68 (MQ=255)
gTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAg < 1:4587480/71‑1 (MQ=255)
ttGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTc < 1:3018093/37‑1 (MQ=255)
tGCCACGGTAAAGCCAAGCTCACCGAAGCAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGAc > 1:4550352/1‑71 (MQ=255)
tGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTa > 1:2122082/1‑52 (MQ=255)
tGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGa > 1:636219/1‑70 (MQ=255)
tGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGAc > 1:185441/1‑71 (MQ=255)
gCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGAcc > 1:4457417/1‑71 (MQ=255)
ccACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATgg < 1:3643679/48‑1 (MQ=255)
cACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACgg > 1:990776/1‑52 (MQ=255)
aCGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGAccgcc < 1:3552261/71‑1 (MQ=255)
cGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATa > 1:3084624/1‑35 (MQ=255)
gTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGa < 1:1114995/40‑1 (MQ=255)
gTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGa < 1:1997832/40‑1 (MQ=255)
gTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGtt < 1:1985603/71‑1 (MQ=255)
aaaGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGttt > 1:3685670/1‑70 (MQ=255)
aaGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATg < 1:4440401/56‑1 (MQ=255)
aaGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTc < 1:3195748/71‑1 (MQ=255)
aaGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTc < 1:2579813/71‑1 (MQ=255)
gCCAAGCTCACCGAAGCAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGtttt < 1:2394023/68‑1 (MQ=255)
gCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGc < 1:1368271/55‑1 (MQ=255)
aaGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCgg > 1:1209968/1‑48 (MQ=255)
aaGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTCAATGc < 1:3083473/71‑1 (MQ=255)
tCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTCAATGcgac > 1:3641884/1‑70 (MQ=255)
tCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTCAATGcgac > 1:376401/1‑70 (MQ=255)
aCCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTCAATGcgacg < 1:597000/69‑1 (MQ=255)
aCCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTCAATGcgacg < 1:1469881/69‑1 (MQ=255)
aCCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTCAATGCgacgac < 1:1911817/71‑1 (MQ=255)
gaagaaACTTTCGATACGGTCGATGGTACGGGTaa > 1:3210134/1‑35 (MQ=255)
gaagaaACTTTCGATACGGTCGATGGTACGGGTAACCGGa > 1:2783119/1‑40 (MQ=255)
aaaCTTTCGATACGGTCGATGGTACGGGTAACCGGATGCa > 1:4634149/1‑40 (MQ=255)
|
GCATCGAAGTTATGATAATCGTCTTCGATTTCCGGCCCGGTTGCCACGGTAAAGCCAAGCTCACCGAAGAAACTTTCGATACGGTCGATGGTACGGGTAACCGGATGCAGACCGCCGTTTTCAATGCGACGAC > W3110S.gb/1800232‑1800364
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
