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 F8 I0 R1
|
311 |
50.1 |
4085234 |
95.9% |
3917739 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,824,257 |
T→C |
40.4% |
F29S (TTT→TCT) |
nadE → |
NAD synthetase, NH3/glutamine‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,824,257 | 0 | T | C | 40.4%
| 28.1
/ 61.4
| 52 | F29S (TTT→TCT) | nadE | NAD synthetase, NH3/glutamine‑dependent |
| Reads supporting (aligned to +/- strand): ref base T (16/15); new base C (13/8); total (29/23) |
| Fisher's exact test for biased strand distribution p-value = 5.73e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATAAAGGCGCTGGGCGCAAAACCGCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGTCAGGAC > W3110S.gb/1824193‑1824327
|
ataaAGGCGCTGGGCGCAAAACCGCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGa < 1:3873346/70‑1 (MQ=255)
ataaAGGCGCTGGGCGCAAAACCGCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGa < 1:1380566/70‑1 (MQ=255)
gcTGGGCGCAAAACCGCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGaaa < 1:1794191/64‑1 (MQ=255)
cAAAACCGCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGaa < 1:811841/55‑1 (MQ=255)
cAAAACCGCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTCTCTGAAAAGCTACCTGCaa > 1:3021488/1‑68 (MQ=255)
cAAAACCGCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTCTCTGAAAAGCTACCTGCAAACt > 1:1211251/1‑71 (MQ=255)
aCCGCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATc > 1:3906816/1‑71 (MQ=255)
gCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGt > 1:2872197/1‑71 (MQ=255)
gCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGt > 1:722043/1‑71 (MQ=255)
cAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTATCCGtt < 1:3672005/71‑1 (MQ=255)
aGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGtt < 1:2571231/70‑1 (MQ=255)
gATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCaa < 1:2720963/58‑1 (MQ=255)
ttAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAAc > 1:3394245/1‑58 (MQ=255)
tAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATc > 1:1271335/1‑62 (MQ=255)
tAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTCTCTGAAAAg > 1:3943812/1‑45 (MQ=255)
aaTGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAg > 1:2109856/1‑44 (MQ=255)
aaTGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTa > 1:3373402/1‑47 (MQ=255)
aaTGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTa < 1:2568675/70‑1 (MQ=255)
aaTGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTa < 1:3190799/70‑1 (MQ=255)
aaTGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTa > 1:2686011/1‑70 (MQ=255)
aaTGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTa > 1:2618041/1‑70 (MQ=255)
aaTGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCAGAAAAGc > 1:2111747/1‑45 (MQ=255)
tGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAAt < 1:1596125/71‑1 (MQ=255)
tGCTGAAGAGGAAATTCGTCGTAGTGTCGATTCTCTGaa < 1:1121415/39‑1 (MQ=255)
tGCTGAAGAGGAAATTCGTCGTAGTGTCGATTCTCTGaa < 1:987477/39‑1 (MQ=255)
cTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCaag > 1:1510627/1‑50 (MQ=255)
agagGAAATTCGTCGTAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTa < 1:1405311/62‑1 (MQ=255)
gAAATTCGTCGTAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCAc < 1:273425/64‑1 (MQ=255)
gAAATTCGTCGTAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGc > 1:872684/1‑70 (MQ=255)
aTTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTaaa < 1:656154/57‑1 (MQ=255)
ttCGTCGTAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTa < 1:2682300/43‑1 (MQ=255)
cgtcgtAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTATc > 1:1481244/1‑43 (MQ=255)
cgtcgtAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTATc > 1:3963833/1‑43 (MQ=255)
cgtcgtAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTATc > 1:647039/1‑43 (MQ=255)
cgtcgtAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTATc > 1:3096286/1‑43 (MQ=255)
tcgtAGTGTCGATTCTCTGAAAAGCTACCTGCAAACt < 1:369356/37‑1 (MQ=255)
gtAGTGTCGATTCTCTGAAAAGCTACCTGCAAACTTa > 1:3781069/1‑37 (MQ=255)
aGTGTCGATTTTCTGAAAAGCTACCTGAAAACTTATCCGtt < 1:895864/41‑1 (MQ=255)
tgtCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTa < 1:3201794/44‑1 (MQ=255)
tCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTg > 1:1535140/1‑50 (MQ=255)
tCGATTCTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTa < 1:2625167/42‑1 (MQ=255)
tCGATTCTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGt > 1:1555797/1‑71 (MQ=255)
tCGATTCTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGt > 1:448034/1‑71 (MQ=255)
tCGATTCTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGt > 1:3511087/1‑71 (MQ=255)
gATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGt > 1:2075307/1‑69 (MQ=255)
gATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGt > 1:685494/1‑69 (MQ=255)
gATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGt > 1:3108594/1‑69 (MQ=255)
gATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGt > 1:303711/1‑69 (MQ=255)
gATTCTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTaaa > 1:3121532/1‑42 (MQ=255)
aTTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACt < 1:2939702/46‑1 (MQ=255)
aTTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGTCAg < 1:4029052/71‑1 (MQ=255)
aTTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGTCAg < 1:933384/71‑1 (MQ=255)
ttCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGTCAGGAc > 1:2307470/1‑71 (MQ=255)
|
ATAAAGGCGCTGGGCGCAAAACCGCAGATTAATGCTGAAGAGGAAATTCGTCGTAGTGTCGATTTTCTGAAAAGCTACCTGCAAACTTATCCGTTCATTAAATCACTGGTGCTCGGGATCAGCGGCGGTCAGGAC > W3110S.gb/1824193‑1824327
|
| 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
