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 F16 I1 R1
|
9 |
28.1 |
657842 |
93.6% |
615740 |
139.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,010,363 |
C→T |
C146Y (TGT→TAT) |
USA300HOU_RS10125 ← |
Putative multidrug export ATP‑binding/permease protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,010,363 | 0 | C | T | 91.7%
| 22.9
/ ‑3.8
| 12 | C146Y (TGT→TAT) | USA300HOU_RS10125 | Putative multidrug export ATP‑binding/permease protein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (4/7); minor base A (1/0); total (5/7) |
| Fisher's exact test for biased strand distribution p-value = 4.17e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.85e-01 |
TACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTG > USA300TCH1516_ALE/2010264‑2010487
|
tatacgtttAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATc < 1:248582/133‑1 (MQ=255)
gTTAAAATGTAAACTGGGAAGATAAACAGTTCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAAGCTATCCAAATATTCATTAACCCTGTTAAAATGAAATTTtttgt < 2:115768/140‑1 (MQ=255)
tgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGAGCAATAATAGTTGTAAAGAAAATGAACCTAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCa > 1:140967/1‑140 (MQ=255)
gtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCaa > 2:276606/1‑140 (MQ=255)
gtaaaatgGGAAGATAAACAGTACTGCTAAAGTCAATATCACATCTAAAAAGAACATTAGGGATAGTGCAATACTACTTATTATATAATCTAACCAAATATTCATAACCCCAGTTAACATGAAATCTTTTGTTTGTTCaa > 2:284226/1‑140 (MQ=255)
aaaCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActc < 1:48622/140‑1 (MQ=255)
gctgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGatat > 2:264336/1‑140 (MQ=255)
ctcactccacaTCTAAAAAGATCATTATGGACATATCAATAATAATTGTTATATAATCTAAGCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCt < 2:310867/133‑1 (MQ=255)
gAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaa < 1:60671/139‑1 (MQ=255)
gAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaa > 2:60671/1‑139 (MQ=255)
ataataatTGTTATATAATCTATCCAAATATTCATTCTGCCGTTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg < 1:10767/140‑1 (MQ=255)
ataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg < 1:187191/140‑1 (MQ=255)
|
TACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTG > USA300TCH1516_ALE/2010264‑2010487
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
