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 F169 I1 R1
|
62 |
44.4 |
970160 |
98.1% |
951726 |
147.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
1,324,256 |
(A)9→8 |
coding (1028/2010 nt) |
mutL → |
DNA mismatch repair protein MutL |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,324,248 | 0 | A | . | 88.6%
| 155.9
/ 15.9
| 44 | coding (1020/2010 nt) | mutL | DNA mismatch repair protein MutL |
| Reads supporting (aligned to +/- strand): ref base A (1/4); new base . (15/24); total (16/28) |
| Fisher's exact test for biased strand distribution p-value = 6.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGACGTAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAAAACGATGA > USA300TCH1516_ALE/1324110‑1324391
|
agACGTAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATGAATTCCTAAATATAACTTGGATTATGTGCCaaaaaaaata < 3:373592/148‑3 (MQ=255)
cGTAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAg > 3:84666/1‑148 (MQ=255)
gTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGAATTATGTGCC‑AAAAAAAATAAAg > 1:3306/1‑141 (MQ=255)
tCATCCAACAAAACTAGAAGTGCGTGTAGGAGATGAAGAGCAACTATACCAATAGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTAcatt > 4:190691/1‑148 (MQ=255)
aacaaAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑TAAAAAAATAAAGTATTAcat < 1:48452/141‑1 (MQ=255)
aaCTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGaacaa > 3:41050/1‑148 (MQ=255)
gAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACaaaa > 3:396908/1‑148 (MQ=255)
gTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACaaaa > 2:27614/1‑141 (MQ=255)
ttATCAAAAGAAGAGCAACTATACCAATTGATTGTAAGCAAAATACAAAAAGCATTTAAAGACCGAATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTAATACATTCATTCGAACAACAAAAAATCGAAtt < 3:391307/148‑1 (MQ=255)
aTCAAAAGAAGAGCAACTTTACCAATTGATAGGGAGCAAAATACAAGAAGCATTTAAAGACAGTATATTAATTTCTAAAAATAACTTGGAAAAAAAG‑AAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTg < 4:161152/148‑1 (MQ=255)
aaaGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGTATTATGTACC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACa < 3:389199/148‑1 (MQ=255)
agaagaGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACaaa < 4:174731/148‑1 (MQ=255)
aagaGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACATCAAAAAATCGAATTTGAACAAAGa < 4:165546/148‑1 (MQ=255)
aagaGCAAATATAACAATTGATTGTGACAAAAATACAAGAAGCATTTAAAGACCGTATATTAATACATAAAAATAACTTGGATTATATGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGa < 4:79300/148‑1 (MQ=255)
aagaGAAACAATAACAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACAGTATATTAATTCCTAAAAATAACTTGGA‑AAAAAAAAAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGa < 4:160173/148‑1 (MQ=255)
agCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACaa < 3:60575/148‑1 (MQ=255)
agCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACaa < 3:58260/148‑1 (MQ=255)
tataCCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAAcaca < 3:286173/148‑1 (MQ=255)
ataCCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACag < 4:143640/148‑1 (MQ=255)
ataCCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCATATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACag < 4:269953/148‑1 (MQ=255)
ttgattgTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATaa > 3:164570/1‑148 (MQ=255)
ttgattgTGAGAAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGA‑TAAAAAAAAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATaa < 4:27870/148‑1 (MQ=255)
attgTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACCGAGAATAACCa < 4:333843/148‑1 (MQ=255)
gAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAgaga > 3:154726/1‑148 (MQ=255)
aCAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGtttt > 4:337733/1‑148 (MQ=255)
gaagCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTAAGAG‑CAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATc < 4:41820/148‑1 (MQ=255)
gCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTG‑CAAAAAAAAATAAAGTAATACATTAATTCGAACAACAAAAAATCGAATATGAACAAAGACAAAACACAGAGAAAAACCAAGAAAAGACGattt > 2:53862/1‑141 (MQ=255)
tttAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTgaaga < 3:246268/148‑1 (MQ=255)
tttAAAGACCGTATATCAATGCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTgaaga < 3:127817/148‑1 (MQ=255)
aaGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGt < 3:190691/148‑1 (MQ=255)
tataTTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGt < 1:27614/141‑1 (MQ=255)
tataTTAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTa < 4:396908/148‑1 (MQ=255)
tAATTCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCa < 4:59827/148‑1 (MQ=255)
ttCCTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCAttt < 3:284519/148‑1 (MQ=255)
atCCTAAAAATAACTAGGAATATGAGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAAAAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCAttt < 4:2264/147‑1 (MQ=255)
cTAAAAATAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATg < 4:154354/148‑1 (MQ=255)
aaaaaTAACTTGGATTATGTGCC‑AAAAAAAATAAAGTATTGCATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAACACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGga > 3:216915/1‑148 (MQ=255)
cTTGGATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATc > 3:81988/1‑148 (MQ=255)
ggATTATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCaaa > 3:152162/1‑148 (MQ=255)
ttATGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAAAACg < 4:364009/148‑1 (MQ=255)
aTGTGCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCa < 2:51984/141‑1 (MQ=255)
gtgCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCATAACGAAga > 3:105874/1‑148 (MQ=255)
gtgCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAAAACGATga > 3:153487/1‑148 (MQ=255)
gtgCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAAAACGATga > 4:47705/1‑148 (MQ=255)
gtgCC‑AAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAAAACGATga < 3:114620/148‑1 (MQ=255)
|
AGACGTAAATGTTCATCCAACAAAACTAGAAGTGCGTTTATCAAAAGAAGAGCAACTATACCAATTGATTGTGAGCAAAATACAAGAAGCATTTAAAGACCGTATATTAATTCCTAAAAATAACTTGGATTATGTGCCAAAAAAAAATAAAGTATTACATTCATTCGAACAACAAAAAATCGAATTTGAACAAAGACAAAACACAGAGAATAACCAAGAGAAGACGTTTTCATCTGAAGAAAGTAACAGTAAGCCATTTATGGAAGAAAATCAAAACGATGA > USA300TCH1516_ALE/1324110‑1324391
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
