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 |
2,499,275 |
T→C |
100% |
C41C (TGT→TGC) |
ilvN → |
acetolactate synthase I, small subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,499,275 | 0 | T | C | 80.2%
| 96.7
/ 13.9
| 65 | C41C (TGT→TGC) | ilvN | acetolactate synthase I, small subunit |
| Reads supporting (aligned to +/- strand): ref base T (0/13); new base C (29/23); total (29/36) |
| Fisher's exact test for biased strand distribution p-value = 2.59e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.25e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ACCCACGTTTGTGGCCTTTTTGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGCCATATCTGGCTACTGGTCAATGACGACCAGCGTCTGG > minE/2499219‑2499339
|
aCCCCCGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATGCa > 1:2490325/1‑68 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCTGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:1252081/1‑69 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTg > 1:3168737/1‑60 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:979268/1‑69 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:2366123/1‑69 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:2469583/1‑69 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:2741745/1‑69 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:295287/1‑69 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:3025078/1‑69 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:479666/1‑69 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGCTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:768877/1‑69 (MQ=255)
aCCCACGTTTGTGGCCTTTTTGCCCGTCGCGATTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAg > 1:3435892/1‑69 (MQ=255)
ccACGTTTGTGGCCTTTTTGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAgg < 1:1534814/68‑1 (MQ=255)
ccACGTTTGTGGCCTTTTTGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAgg < 1:1558433/68‑1 (MQ=255)
ccACGTTTGTGGCCTTTTTGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAgg < 1:3339337/68‑1 (MQ=255)
ccACGTTTGTGGCCTTTTTGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAgg < 1:2522245/68‑1 (MQ=255)
cTTTTTGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGc < 1:309266/69‑1 (MQ=255)
cTTTTTGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGc < 1:74488/69‑1 (MQ=255)
cTTTTTGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGc < 1:2808436/69‑1 (MQ=255)
ttttGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGCCa < 1:2751253/69‑1 (MQ=255)
ccgcGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGCCATATCTGGCt < 1:2365219/69‑1 (MQ=255)
ccgcGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGCCATATCTGGCt < 1:1420857/69‑1 (MQ=255)
ccgcGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGCCATATCTGGCt < 1:2673054/69‑1 (MQ=255)
ccgcGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGCCATATCTGGCt < 1:1675384/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:2285439/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:827241/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:1280046/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:722486/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:1431411/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:3386407/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:160179/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:3069841/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:2935262/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:2888197/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:2513609/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:1020739/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:2258635/69‑1 (MQ=255)
cTTTTAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:2249797/69‑1 (MQ=255)
ttttAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:1794634/68‑1 (MQ=255)
ttttAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:1696039/68‑1 (MQ=255)
ttttAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:3351464/68‑1 (MQ=255)
ttttAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:383060/68‑1 (MQ=255)
ttttAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:3025838/68‑1 (MQ=255)
ttttAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:54471/68‑1 (MQ=255)
ttttAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:1466063/68‑1 (MQ=255)
tAACGTTTAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGCCATATCTGGCt < 1:2864696/60‑1 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:1189577/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:2235071/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:637253/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:3321198/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:22770/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:918133/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:945077/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:1083857/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:1883640/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:2808826/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:3302426/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:3208669/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:2605327/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:2611434/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:2736170/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:3018972/1‑68 (MQ=255)
tAACGTTGAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTGGTCa > 1:283826/1‑68 (MQ=255)
gAAGGCATTCTCTGCCTGCCGATTCAGGACAGCGACAAAAGCCACATCTGGCTACTgg < 1:2979480/58‑1 (MQ=255)
tctcTGCCTGACGATTCAGGACAGCGACAAAAGCCACATCTGGCTACCgg < 1:1462347/50‑1 (MQ=255)
tCTGCCGATTCAGGACAGCGACAAAAGCCATATCTGGCTACTGGTCAATGACGACCAGCGTCTgg > 1:3280902/1‑65 (MQ=255)
|
ACCCACGTTTGTGGCCTTTTTGCCCGCCGCGCTTTTAACGTTGAAGGCATTCTTTGTCTGCCGATTCAGGACAGCGACAAAAGCCATATCTGGCTACTGGTCAATGACGACCAGCGTCTGG > minE/2499219‑2499339
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
