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 |
2,502,887 |
(A)5→6 |
coding (1411/2106 nt) |
melR_2 → |
Melibiose operon regulatory protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,502,882 | 1 | . | A | 96.9%
| 109.8
/ ‑2.6
| 32 | coding (1406/2106 nt) | melR_2 | Melibiose operon regulatory protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base A (12/19); total (12/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01 |
TCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGT > USA300TCH1516_ALE/2502736‑2503010
|
tCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTTAAAATTC‑a > 3:84941/1‑148 (MQ=255)
aaaattaaaaACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaaa‑aact < 4:17612/148‑4 (MQ=255)
aattaaaaACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaaa‑aactgc > 4:188087/1‑143 (MQ=255)
aaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACAt < 3:244594/148‑1 (MQ=255)
aaaaaTAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCtt < 3:368288/148‑1 (MQ=255)
aTAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACAt > 1:45012/1‑141 (MQ=255)
aTTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAAc < 3:273836/148‑1 (MQ=255)
aTTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTAATCAAACATAAAACAAGTTTATAATGTCATGCAGCGTCTAAAATTCCATTACTACTTTATTTATAAAAAAAAATAAAAAA‑ACTGCAACACAACTTAACACTAAAAAc < 4:240870/148‑1 (MQ=255)
aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAac > 3:249376/1‑148 (MQ=255)
aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAac > 3:238454/1‑148 (MQ=255)
aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAac > 4:309489/1‑148 (MQ=255)
aGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAAc > 3:386394/1‑148 (MQ=255)
cGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGa < 4:263328/148‑1 (MQ=255)
cGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGa < 3:49801/148‑1 (MQ=255)
aTGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGaca < 3:46049/148‑1 (MQ=255)
ggCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACt > 3:248183/1‑148 (MQ=255)
tttttAGAAACTTATTCAAACGTGAAACAAGTTTATAATGACATTCAGCATCTTAAATTCCATTATTACTTTATTAATAAAAAAAAATCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAt < 4:286858/148‑1 (MQ=255)
ttAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAtttt < 4:301221/148‑1 (MQ=255)
ttACAAACTTATTCAACCGAGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAACACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGacac < 2:50730/141‑1 (MQ=255)
aaCTTATTCACCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa < 3:355651/148‑1 (MQ=255)
aaCTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa < 3:355653/148‑1 (MQ=255)
cAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGa < 4:248183/148‑1 (MQ=255)
aaCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGaa < 3:380535/148‑1 (MQ=255)
tGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAattta < 4:347847/148‑1 (MQ=255)
ggAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAatttat < 3:149173/148‑1 (MQ=255)
aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTAtttt > 4:195533/1‑148 (MQ=255)
cAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTa < 4:125307/148‑1 (MQ=255)
tttATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGAtt > 3:51289/1‑148 (MQ=255)
gTCATGCAGCGTCTTAAATTCCATTAGTACTTTATTGATAAAAAAAAAACAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGtata < 4:45503/148‑1 (MQ=255)
tAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAAtt < 4:109694/148‑1 (MQ=255)
tAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAAtt < 4:46386/148‑1 (MQ=255)
ccATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGtata > 4:1077/1‑148 (MQ=255)
tattaCTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat > 4:361432/1‑148 (MQ=255)
tactaCTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat > 4:98863/4‑148 (MQ=255)
ttATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACctgt > 3:148889/1‑148 (MQ=255)
|
TCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGT > USA300TCH1516_ALE/2502736‑2503010
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
