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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,079,041 |
A→G |
52.7% |
I417I (ATT→ATC) |
tktA ← |
transketolase 1, thiamin‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,079,041 | 0 | A | G | 52.7%
| 13.2
/ 104.1
| 74 | I417I (ATT→ATC) | tktA | transketolase 1, thiamin‑binding |
| Reads supporting (aligned to +/- strand): ref base A (4/31); new base G (13/26); total (17/57) |
| Fisher's exact test for biased strand distribution p-value = 2.99e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01 |
GAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTT > W3110S.gb/3078981‑3079103
|
gAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGt < 1:2860679/69‑1 (MQ=255)
gAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGt < 1:2987039/69‑1 (MQ=255)
gAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGt < 1:2397150/69‑1 (MQ=255)
gAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGt < 1:1559730/69‑1 (MQ=255)
gAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGt < 1:2288662/69‑1 (MQ=255)
gAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGt < 1:827682/69‑1 (MQ=255)
aCATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCa > 1:1915930/1‑69 (MQ=255)
tCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATa > 1:683102/1‑68 (MQ=255)
tCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATa > 1:2660543/1‑68 (MQ=255)
cAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCa > 1:3596798/1‑55 (MQ=255)
cAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCa < 1:1438300/55‑1 (MQ=255)
aGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCg < 1:2039798/69‑1 (MQ=255)
aGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCg < 1:2207676/69‑1 (MQ=255)
aGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCg < 1:3270699/69‑1 (MQ=255)
gAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGGGGTCAt < 1:7385/63‑1 (MQ=255)
gAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCAt < 1:2285301/63‑1 (MQ=255)
gAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCAt < 1:1615546/63‑1 (MQ=255)
gAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCAt < 1:3095404/63‑1 (MQ=255)
gAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGa < 1:2346667/68‑1 (MQ=255)
gAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGa < 1:3055278/68‑1 (MQ=255)
gAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGa < 1:1088487/68‑1 (MQ=255)
gAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg > 1:2706441/1‑68 (MQ=255)
ggTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGaa < 1:705037/68‑1 (MQ=255)
ggTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGaa < 1:3119091/68‑1 (MQ=255)
gtACGGCAGGAATCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGaa < 1:2122055/65‑1 (MQ=255)
gtACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAacac > 1:890847/1‑68 (MQ=255)
gtACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGaa < 1:1314588/65‑1 (MQ=255)
gtACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGaa < 1:563465/65‑1 (MQ=255)
gtACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGaa < 1:3463285/65‑1 (MQ=255)
gtACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGaa < 1:1007477/65‑1 (MQ=255)
gtACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGaa < 1:117648/65‑1 (MQ=255)
gtACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAacac > 1:2411367/1‑68 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAacac > 1:1604002/1‑67 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAacac > 1:3331942/1‑67 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCg < 1:337183/69‑1 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCg < 1:2925504/69‑1 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCg < 1:1166133/69‑1 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCg < 1:3494098/69‑1 (MQ=255)
cGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGt < 1:275435/68‑1 (MQ=255)
cGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTa > 1:1348741/1‑69 (MQ=255)
gcagcaAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGt < 1:1322751/43‑1 (MQ=38)
gCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGt < 1:905092/43‑1 (MQ=255)
gCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGt < 1:1055450/43‑1 (MQ=255)
gCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGt < 1:2799382/43‑1 (MQ=255)
gCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATTCCGa < 1:3059765/51‑1 (MQ=255)
cAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTg < 1:2990188/69‑1 (MQ=255)
aGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGt < 1:1711068/69‑1 (MQ=255)
aGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGt < 1:1542854/69‑1 (MQ=255)
aGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGt < 1:796458/69‑1 (MQ=255)
aGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGCGGATGt < 1:6550/69‑1 (MQ=255)
aGCCACCGTGCACGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGt < 1:922695/69‑1 (MQ=255)
ccACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGa < 1:762442/43‑1 (MQ=255)
ccACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGa < 1:3309198/43‑1 (MQ=255)
aCCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGtt > 1:878361/1‑69 (MQ=255)
gTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTAcc > 1:1476807/1‑69 (MQ=255)
gTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTAcc > 1:2370817/1‑69 (MQ=255)
gTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAATTAcc > 1:3100355/1‑69 (MQ=255)
gggAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCgcag < 1:1296879/69‑1 (MQ=255)
gggAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCgcag < 1:3111718/69‑1 (MQ=255)
gggAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCgcag < 1:3420632/69‑1 (MQ=255)
ggAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCgcagc < 1:305873/69‑1 (MQ=255)
aTACCGTTAGCAATCGCGGTCATACCGAACTTGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCt < 1:2462235/69‑1 (MQ=255)
aCCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTc > 1:401038/1‑69 (MQ=255)
aCCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTc > 1:3054851/1‑69 (MQ=255)
aCCGTTAGCGAT‑‑CGGTCATACCGAACTCGCGAaca < 1:2506191/35‑1 (MQ=25)
aCCGTTAGCAATCGCGGTCATACCGAACTCGCGAacac < 1:3185356/38‑1 (MQ=255)
ccGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCgcagc > 1:2481249/1‑62 (MQ=255)
ccGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCg > 1:2862333/1‑69 (MQ=255)
gTTAGCGATCGCGGTAATACAGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt < 1:1904425/69‑1 (MQ=255)
gTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGtt < 1:3225746/51‑1 (MQ=255)
gTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt < 1:462022/69‑1 (MQ=255)
gTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt < 1:504808/69‑1 (MQ=255)
gTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt < 1:2515048/69‑1 (MQ=255)
gTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt < 1:1311489/69‑1 (MQ=255)
gTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt < 1:297927/69‑1 (MQ=255)
ttAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGtt < 1:3282235/50‑1 (MQ=255)
|
GAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTT > W3110S.gb/3078981‑3079103
|
| 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
