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 |
|
A5 F58 I0 R1
|
35 |
61.1 |
1410250 |
95.0% |
1339737 |
139.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,028,508 |
A→T |
22.2% |
V46E (GTA→GAA) |
USA300HOU_RS10230 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,028,508 | 0 | A | T | 22.2%
| 91.3
/ 11.4
| 43 | V46E (GTA→GAA) | USA300HOU_RS10230 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (14/19); new base T (6/4); total (20/23) |
| Fisher's exact test for biased strand distribution p-value = 4.73e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAACGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTC > USA300TCH1516_ALE/2028370‑2028642
|
tAACGCACAATAAGTAATAATAAAAAAACTAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGAAATAAATATCGCGCCTATCCAAAAAGACAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTAc < 2:239988/140‑1 (MQ=255)
cGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAACAGGCCACGTATTTTATGAAAATAAAGATCTcctaccta > 1:244317/1‑140 (MQ=255)
cGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATa > 1:206175/1‑140 (MQ=255)
ttaataaaaaaaaAAAGACGAACAAGATGATCATTGTATACTTATTACACAATAATGTGAATGCAATTAATATCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAAt < 2:153465/136‑1 (MQ=255)
tAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCACAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAAt > 1:574826/1‑140 (MQ=255)
tAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCCCGTATTTTATGAAAATACAGATATCCTTCATAAACCAAt > 1:28352/1‑140 (MQ=255)
tAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAAt < 2:301523/140‑1 (MQ=255)
tAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAAt < 2:409732/140‑1 (MQ=255)
ataataaAAAGACGAACAAGAGGATGATTGTATACTTATTAGACAATAATGTGAATTCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACAt < 2:132440/140‑1 (MQ=255)
taaAAAGACGAACAAGATGATTATTGTAGACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCa < 1:439300/140‑1 (MQ=255)
aGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTCTGAAAATAAAGATATCCTACATAAACTAATACACAACCCaataat > 2:447479/1‑140 (MQ=255)
aGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCaataat > 1:452959/1‑140 (MQ=255)
aCAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACg < 1:632349/140‑1 (MQ=255)
tgatTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAg < 2:206175/140‑1 (MQ=255)
ggatCGTATACTTATTGAACAACAACGTGAATGCAATTAATAGGGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAg < 2:244317/139‑1 (MQ=255)
gatTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGc < 1:672501/140‑1 (MQ=255)
attaAACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCaa < 1:379498/140‑1 (MQ=255)
taGACCAAAATGAGAATTGAATTAATAGTGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATAACCTTCATAAACTAATATACATCACAATAATAGAACGAGTAAAAAGCCAATTTTTTCaaaa < 2:575931/140‑1 (MQ=255)
taGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCaaaa < 1:408680/140‑1 (MQ=255)
taacaatGTGAACGCAATTAATAGCGCGCTGATCCAAAACACCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTACTACACATCCCAATAATAGAACGAGTAAAAAGCCTATTTTTTCAAAAAata < 2:67743/136‑1 (MQ=255)
cAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAata > 2:336210/1‑140 (MQ=255)
aataatGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAatat > 2:100006/1‑140 (MQ=255)
aataatGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATACCAGTAATAGAACGCGTAAAAAGCCAATTTTTTCaaaacacat > 1:196373/1‑135 (MQ=255)
gtgtgAGGGCAATGTAGAGCGGGGCTATCCGAGACGCCAAAAGGCGACGTATTTGATGAAAATAAAGATATCCTACATAAACTAATACGCATCCCAAGAAGAGGAGGAGTAAAGAGCCAAGTTTTGCAAAAAATATgtag < 2:323703/139‑1 (MQ=255)
tgtgAATGCAATCAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATTCACATCCCAATAATAGCACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtagt < 2:92996/140‑1 (MQ=255)
gtgAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtagta > 1:519713/1‑140 (MQ=255)
gggAATGTAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATATACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATgtagta < 2:323058/138‑1 (MQ=255)
agtGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCAAATTTTTTCAAAAAATATGTAGTaaaa > 2:476517/3‑140 (MQ=255)
tAGCGCGCCTATCCAAACCGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAACCCAATCTTTTCCAAAAATCTGGAGTAAAAATTgcacataa > 2:694588/1‑133 (MQ=255)
tAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATACACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATAGGTCGTAACGATTGGCaataa > 1:141130/1‑140 (MQ=255)
tAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAGGCCCATTTTTTCAAAAAATATGTAGTAGAAATTGGCaaaaa > 1:223903/1‑140 (MQ=255)
tAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCATCAAATATGGAGTAAAAATTGGCaataa > 2:111110/1‑140 (MQ=255)
tAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCaataa < 2:335132/140‑1 (MQ=255)
cAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGt > 1:178745/1‑140 (MQ=255)
aaaCGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTaa > 2:650809/1‑140 (MQ=255)
aCGCCAAAAGGCCACGTATTTTCTGAAAATAAAGATATCCCTCATCAACTAATACACATCCCAATAATAGAACCAGTAAAAACCCAATTTCTTCAAACCATATGTCGTAACAATCAGCCATAATCATTAATGCGGTcaaa > 2:140070/1‑140 (MQ=255)
gCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAAt > 2:453802/1‑140 (MQ=255)
ccACTTATTTTATGAAAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAATAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACAt < 2:294565/140‑1 (MQ=255)
ccACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACAt < 2:178745/140‑1 (MQ=255)
cACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGCAAAAAGCCAATTTTTTCACAATATATGTAGGTCAGATGAGCAATAATCATTAATGCAGTAAAAATGATCAACagt > 2:312546/1‑138 (MQ=255)
aCGTCTTTTATGACAATAAAGATATCCTTCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGGAAAAATGATCAACAttt < 2:550498/140‑1 (MQ=255)
aCGTATTTTATTAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATTTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACAttt < 2:353375/140‑1 (MQ=255)
ttATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGa > 2:427188/1‑140 (MQ=255)
atCCAACATAAACAAATACAAAGGAAAATAATAGAACGATTAAAAAGCAAAAAAAAAAAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTc < 2:398154/140‑1 (MQ=255)
|
TAACGCACAATAAGTAATAATAAAAAGACGAACAAGATGATGATTGTATACTTATTAGACAATAATGTGAATGCAATTAATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTC > USA300TCH1516_ALE/2028370‑2028642
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
