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 |
|
A2 F17 I0 R2
|
278 |
43.2 |
2215644 |
94.6% |
2095999 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,680,754 |
T→C |
31.8% |
Y1407C (TAC→TGC) |
yfhM ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,680,754 | 0 | T | C | 31.8%
| 49.0
/ 37.0
| 44 | Y1407C (TAC→TGC) | yfhM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (18/12); new base C (7/7); total (25/19) |
| Fisher's exact test for biased strand distribution p-value = 7.45e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.00e-02 |
ACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTCGCGCAGTGAAC > minE/1680690‑1680823
|
aCTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGc > 1:2026805/1‑70 (MQ=255)
aCTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCt > 1:1439537/1‑71 (MQ=255)
aCTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCt > 1:891930/1‑71 (MQ=255)
tttCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGCACTGCt < 1:1340502/69‑1 (MQ=255)
cGATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGCACTGCTCATCGGGTAg > 1:1920102/1‑69 (MQ=255)
gATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAg > 1:349897/1‑71 (MQ=255)
gATAGACAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAg > 1:367798/1‑71 (MQ=255)
aTAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGt > 1:488016/1‑71 (MQ=255)
gCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGc < 1:1810335/65‑1 (MQ=255)
gCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAttt > 1:944414/1‑70 (MQ=255)
gCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGCACTGCTCATCGGGTAGCAGTTTAtttt < 1:958785/71‑1 (MQ=255)
ccAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAg > 1:342919/1‑71 (MQ=255)
aaaCGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCa > 1:2081416/1‑68 (MQ=255)
aaaCGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGc > 1:506337/1‑70 (MQ=255)
aaaCGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCa < 1:1350392/71‑1 (MQ=255)
aaaCGCATGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGc > 1:825/1‑70 (MQ=255)
aCGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAg < 1:252491/71‑1 (MQ=255)
ctgctgCGAAAGTGTGTTCAGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGgaga < 1:813946/71‑1 (MQ=255)
gctgcGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGagag > 1:393189/1‑70 (MQ=255)
ctgcGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGagag < 1:1165617/69‑1 (MQ=255)
gcGAAAGTGTGTTCAGCAAAGTGCACTGCTCATCGGTTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCAt > 1:750807/1‑70 (MQ=255)
gcGAAAGTGTGTTCAGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCAt > 1:2090543/1‑70 (MQ=255)
cGAAAGTGTGTTCAGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTttctt < 1:1495987/53‑1 (MQ=255)
cGAAAGTGTGTTCAGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCAtt < 1:1281651/70‑1 (MQ=255)
gAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTaa > 1:1192433/1‑71 (MQ=255)
aaaGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGc < 1:1647108/56‑1 (MQ=255)
aaGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAAcg < 1:2066762/71‑1 (MQ=255)
gtgtgtTCAGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTTTCTTCCATCAAGGAGAGCATTAAcgcg > 1:395456/1‑71 (MQ=255)
ttCAGCAAAGTGTACTGCTCATCTGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAAcg < 1:1079299/64‑1 (MQ=255)
ttCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAAc < 1:2157139/63‑1 (MQ=255)
ttCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTc > 1:1982487/1‑71 (MQ=255)
ttCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTc > 1:1842898/1‑71 (MQ=255)
cAGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAAcgc > 1:1916309/1‑63 (MQ=255)
cAGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTcg > 1:237261/1‑70 (MQ=255)
aGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCa < 1:1729421/46‑1 (MQ=255)
aGCAAAGTGCACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCa < 1:1164958/46‑1 (MQ=255)
cAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTcgcg > 1:643240/1‑69 (MQ=255)
cAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTcgcg > 1:994526/1‑69 (MQ=255)
aaGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTaa > 1:1976261/1‑55 (MQ=255)
aaGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTaa > 1:1702830/1‑55 (MQ=255)
aGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCGAGCAAGGAGAGCATTAACGCGTTGTCGCGCAGTg < 1:1154992/71‑1 (MQ=255)
aGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTCGCGCAGTg < 1:200321/71‑1 (MQ=255)
aGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTCGCGCAGTg < 1:1805036/71‑1 (MQ=255)
aGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTCGCGCAGTg < 1:1090517/71‑1 (MQ=255)
gtgtACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTCGCGCAGTg > 1:977354/1‑70 (MQ=255)
tACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTCGCGCAGTGAAc < 1:309873/70‑1 (MQ=255)
tACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTCGCGCAGTGAAc < 1:1504272/70‑1 (MQ=255)
|
ACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATTTTCTTCCAGCAAGGAGAGCATTAACGCGTTGTCGCGCAGTGAAC > minE/1680690‑1680823
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
