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 I1 R1
|
12 |
20.5 |
473580 |
94.8% |
448953 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
1,535,291 |
G→A |
Q14* (CAA→TAA) |
lapB ← |
Lipopolysaccharide assembly protein B |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,535,291 | 0 | G | A | 95.2%
| 60.6
/ NA
| 21 | Q14* (CAA→TAA) | lapB | Lipopolysaccharide assembly protein B |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (10/10); minor base T (0/1); total (10/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CACGCGGAATACTTCCAAACCTTGTGGCATTAATCCAAAATTGTAAAGTGTCTCTCCTAGAATAAATAATGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTGTAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATCCTGGAAATGATACATTTACAGCATCAAATTGTTTGATTTTGACAGGCT > USA300TCH1516_ALE/1535160‑1535425
|
cacGCGGAATACTTCCAAACCTTGTGGCATTAATCCAAAATTGTAAAGTGTCTCTCCTAGAATAAATAATGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGCTTTTATAGATTGat > 1:3374/1‑141 (MQ=255)
aTACTTCCAAACCTTGTGGCATTAATCCAAAATTGTAAAGTGTCTCTCCTAGAATAAATAATGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTa > 2:65081/1‑141 (MQ=255)
cTTGTGGCATTAATCCAAAATTGTAAAGTGTCTCTCCTAGAATAAATAATGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGa > 2:12697/1‑141 (MQ=255)
ttGTGGCATTAATCCAAAATTGTAAAGTGTCTCTCCTAGAATAAATAATGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGat > 1:145547/1‑141 (MQ=255)
ccAAAATTGTAAAGTGTCTCTCCTAGAATAAATAATGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTta < 2:184075/141‑1 (MQ=255)
tGTAAAGTGGCTCTCCTAGAATAAATAATGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATc < 1:182020/141‑1 (MQ=255)
tctcCTAGAATAAATAATGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCt > 1:146820/1‑141 (MQ=255)
tcCTAGAATAAATACTGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTaa < 1:129353/141‑1 (MQ=255)
atGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTg < 2:123790/141‑1 (MQ=255)
tGCGTCATCGTTGTCAGTAGTTATTGCGTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTgg < 1:7602/141‑1 (MQ=255)
cGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATc > 1:145723/1‑141 (MQ=255)
gTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATcc < 2:188746/141‑1 (MQ=255)
ttGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATCCt < 1:11468/141‑1 (MQ=255)
gtTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTTTAAGCCGGTATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATCCTGGAAATGAt < 2:167481/141‑1 (MQ=255)
gtTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATCCTGGAAATGAt > 1:11670/1‑141 (MQ=255)
ttATTGGTTCTTTATCACGAGAGTCTAAATTTTGTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATCCTGGAAATGATa < 2:81701/141‑1 (MQ=255)
cacGAGAGTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATCCTGGAAATGATACATTTACAGCATCaa > 1:45212/1‑141 (MQ=255)
gagTCTAAATTTTCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTTTTAAAATTCCTGGAAATAATACATTTACACCATCAAAtttt > 2:234225/1‑139 (MQ=255)
tttCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATCCTGGAAATGATACATTTACAGCATCAAATTGTTTGATTTTGa < 1:204264/141‑1 (MQ=255)
ttCTAGTTTTTATAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATCCTGGAAATGATACATTTACAGCATCAAATTGTTTGATTTTGAc < 1:12697/141‑1 (MQ=255)
gTTTTTATAGATTGATATCGTCTATTAATTTATAGATAACTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGATTGGGTAGAAATCCTGGAAATGATACATTTACAGCATCAAATTGTTTGATTTTGACAGGCt > 1:197636/1‑141 (MQ=255)
|
CACGCGGAATACTTCCAAACCTTGTGGCATTAATCCAAAATTGTAAAGTGTCTCTCCTAGAATAAATAATGCGTCATCGTTGTCAGTAGTTATTGCTTCATTAACACGAGAGTCTAAATTTTCTAGTTTTTGTAGATTGATATCGTCTATTAATTTATAGATATCTTCCATTTTATATTATCCCTCATTTTCTAAAAGCTTTAGTTTTGGTAAAAATCCTGGAAATGATACATTTACAGCATCAAATTGTTTGATTTTGACAGGCT > USA300TCH1516_ALE/1535160‑1535425
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
