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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,716,836 |
A→G |
15.0% |
intergenic (+94/+104) |
yphH → / ← glyA |
predicted DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,716,836 | 0 | A | G | 15.0%
| 179.2
/ 18.9
| 77 | intergenic (+94/+104) | yphH/glyA | predicted DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (27/37); new base G (5/5); total (33/44) |
| Fisher's exact test for biased strand distribution p-value = 7.37e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGAAGGAAGCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAAC > minE/1716769‑1716906
|
cGAAGGAAGCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑At > 1:2109193/1‑71 (MQ=255)
gaaggaagCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑Att > 1:908025/1‑71 (MQ=255)
aaggaagCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTg < 1:3069839/71‑1 (MQ=255)
aggaagCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGgag‑a > 1:2899006/1‑67 (MQ=255)
aggaagCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTg > 1:3893846/1‑70 (MQ=255)
ccTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAatata < 1:390253/71‑1 (MQ=255)
gatgatCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAata > 1:215936/1‑65 (MQ=255)
atgatCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGaa < 1:1686696/71‑1 (MQ=255)
atgatCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGa < 1:2902147/70‑1 (MQ=255)
tgatCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAAt < 1:3394466/71‑1 (MQ=255)
atCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATAtt < 1:3312726/65‑1 (MQ=255)
atCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAAttt > 1:3644204/1‑71 (MQ=255)
tCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGgag‑a > 1:3415532/1‑52 (MQ=255)
tCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGgag < 1:3756696/51‑1 (MQ=255)
tCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTg > 1:205316/1‑71 (MQ=255)
cATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAAtt < 1:1567423/68‑1 (MQ=255)
aTAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGc > 1:2747197/1‑70 (MQ=255)
aaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGga < 1:3535926/45‑1 (MQ=255)
aaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCa < 1:2641892/52‑1 (MQ=255)
aCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAatata < 1:1557983/56‑1 (MQ=255)
aCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAatata < 1:2154115/56‑1 (MQ=255)
aCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGt > 1:2554609/1‑71 (MQ=255)
cGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGtt > 1:1456999/1‑71 (MQ=255)
cGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGtt > 1:3195851/1‑71 (MQ=255)
aaaaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAAt < 1:1120278/59‑1 (MQ=255)
caaaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTg < 1:2660934/70‑1 (MQ=11)
aaaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTg < 1:2893220/71‑1 (MQ=255)
aaaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTg > 1:1727867/1‑71 (MQ=255)
agcttGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTg < 1:3602840/67‑1 (MQ=11)
aaaTTGCCTGATGCGCTGCGCTTATCAGGCCTACAAGTTGAATTGCAATTTATTGAAttt > 1:3942993/1‑60 (MQ=1)
aaaTTGCCTGATGCGCTGCGCTTATCAGGCCTACAAGTTGAATTGCAATTTATTGAATTTGCACATTTTTg < 1:1597560/71‑1 (MQ=2)
aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGt < 1:1290110/71‑1 (MQ=255)
gcttGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTg > 1:3071000/3‑69 (MQ=11)
aaTTGCCTGATGCGCTGCGCTTATCAGGCCTACAAGTTGAATTGCAATTTATTGAATTTGCACATTTTTGt < 1:3293701/71‑1 (MQ=0)
aaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTa < 1:2306066/71‑1 (MQ=255)
aaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTa < 1:2052954/71‑1 (MQ=255)
cttGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAg < 1:198412/70‑1 (MQ=11)
cttGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAg < 1:1647948/70‑1 (MQ=11)
cttGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAg < 1:1199022/70‑1 (MQ=11)
ttGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAgg < 1:2345146/71‑1 (MQ=255)
ttGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTGTAgg < 1:1777636/71‑1 (MQ=11)
gCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGcc > 1:533538/1‑71 (MQ=255)
gCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGcc > 1:318986/1‑71 (MQ=255)
cTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCgg < 1:2518958/71‑1 (MQ=255)
cTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCg > 1:1166864/1‑70 (MQ=255)
tGATGCGCGATGCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGa > 1:896482/1‑71 (MQ=11)
gATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAatata > 1:2388512/1‑42 (MQ=255)
gATGCGCGATGCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGa > 1:2193709/1‑70 (MQ=11)
aTGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCa < 1:3548242/36‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCa < 1:3163549/36‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt > 1:1539611/1‑70 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt < 1:1708868/70‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATa < 1:3632001/71‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATa < 1:3098876/71‑1 (MQ=255)
aTGCGCGATGCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGAt < 1:2435653/70‑1 (MQ=11)
tGCGCTACGCTTATCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGAt > 1:83255/1‑69 (MQ=11)
gcgcTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTg < 1:1786627/58‑1 (MQ=255)
cgcTACGCTTATCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAg < 1:920009/70‑1 (MQ=11)
gcTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGc > 1:2081729/1‑71 (MQ=255)
gcTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGc < 1:3736786/71‑1 (MQ=255)
gcTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGc < 1:2621248/71‑1 (MQ=255)
tACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAg > 1:3572999/1‑67 (MQ=255)
gatgCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGt < 1:3627719/68‑1 (MQ=11)
atgCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGtt < 1:3319468/69‑1 (MQ=11)
atgCTTATCAGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGtt < 1:76576/69‑1 (MQ=11)
cGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGtt < 1:650953/70‑1 (MQ=255)
cGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTc < 1:3132762/71‑1 (MQ=255)
cGCTTATCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATaa > 1:2901644/1‑64 (MQ=2)
cGCTTATCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATaa > 1:1928570/1‑64 (MQ=2)
cGCTTATCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCgc < 1:152775/69‑2 (MQ=11)
cGCTTATCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTc > 1:1089706/1‑71 (MQ=2)
cTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAAt > 1:3500498/1‑37 (MQ=255)
ttATCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTcgcg > 1:3753857/1‑71 (MQ=2)
aTCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCa < 1:1702707/39‑1 (MQ=255)
aTCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCa < 1:2962015/39‑1 (MQ=255)
aTCAGGCCTACAAGTGC‑ATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCgct < 1:1792260/65‑3 (MQ=2)
tCAGGCCTACACGGAG‑ATTGCAATATATTTAATTTGCAAAGTTTTGt > 1:108144/1‑47 (MQ=255)
tCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTa > 1:3556636/1‑48 (MQ=255)
aGGCCTACCAGAAG‑ATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGt > 1:2792880/1‑61 (MQ=11)
ggAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCAt > 1:2561440/1‑62 (MQ=255)
ggAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCAt > 1:3395276/1‑62 (MQ=255)
aag‑aTTGCAATATATTGAATTTGCACTGTTTTGTAGGCCg < 1:2694764/39‑1 (MQ=11)
ag‑aTTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGaac < 1:1855622/71‑1 (MQ=11)
|
CGAAGGAAGCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAG‑ATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAAC > minE/1716769‑1716906
|
| 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
