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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,295,693 |
C→T |
100% |
A18T (GCG→ACG) |
ccmH ← |
heme lyase, CcmH subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,295,693 | 0 | C | T | 80.0%
| 82.4
/ 17.7
| 40 | A18T (GCG→ACG) | ccmH | heme lyase, CcmH subunit |
| Reads supporting (aligned to +/- strand): ref base C (7/1); new base T (16/16); total (23/17) |
| Fisher's exact test for biased strand distribution p-value = 1.07e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TCTTCAGTGAGCTGACGGAACTGTTGTTCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGCCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGCCTCCT > W3110S.gb/2295626‑2295757
|
tcttcACTGAGCTGACGGAACTGTTGTTCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAg > 1:1623/1‑71 (MQ=255)
cttcAGTGAGCTGACGGAACTGTTGTTCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAgc > 1:301191/1‑71 (MQ=255)
ggAACTGTTGTTCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGCCAGCGCTGAGCCGGAGat > 1:2618876/1‑70 (MQ=255)
gttgttCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcag > 1:1187688/1‑70 (MQ=255)
ttgttCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagca > 1:1989869/1‑71 (MQ=255)
ttgttCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGCAGATcatcagc < 1:2521667/70‑1 (MQ=255)
tgttCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcat > 1:2058547/1‑71 (MQ=255)
gttCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcat > 1:597130/1‑70 (MQ=255)
ttCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcat < 1:366564/69‑1 (MQ=255)
ttCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcag < 1:2554076/66‑1 (MQ=255)
ccTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcatcag < 1:353289/70‑1 (MQ=255)
ccTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcatcag < 1:1723589/70‑1 (MQ=255)
ccTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcatcag < 1:2002391/70‑1 (MQ=255)
tgCTTCATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCgg > 1:1872531/1‑50 (MQ=255)
cATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcatcag < 1:1741980/61‑1 (MQ=255)
cATCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcatcag < 1:1975183/61‑1 (MQ=255)
aTCTTTAAACTGCAACACATCGATGGTCGCCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAAt < 1:2634964/70‑1 (MQ=255)
tCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcatcag < 1:138790/59‑1 (MQ=255)
tCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagcatcag < 1:1306867/59‑1 (MQ=255)
tCTTTAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCC‑‑AGATcatcagcatcag < 1:1644566/57‑1 (MQ=255)
tttAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATCAtcagcatcagca > 1:1281274/1‑59 (MQ=255)
tAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagca > 1:512596/1‑51 (MQ=255)
tAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagca > 1:75319/1‑51 (MQ=255)
tAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATaaaa < 1:2311679/69‑1 (MQ=255)
tAAACTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATaaa < 1:1554762/68‑1 (MQ=255)
cTGCAACACATCGATGGTCGTCAGCGCTGAGCCGGAGATcatcagca > 1:887122/1‑47 (MQ=255)
tGCAACACATCGATGGTCGCCAGCGCTGAGCCGGAGATcatcagca > 1:1320303/1‑46 (MQ=255)
tGCAACACATCGATGGTCGCCAGCGCTGAGCCGGAGATcatcagca > 1:2128191/1‑46 (MQ=255)
acaTCGATGGTCGCCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCAt > 1:1942490/1‑65 (MQ=255)
aTCGATGGTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATaaa < 1:2137599/55‑1 (MQ=255)
tCGATGGTCGCCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCaa > 1:506275/1‑50 (MQ=255)
gATGGTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATaaaaa > 1:733793/1‑54 (MQ=255)
gATGGTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGcctc < 1:928281/71‑1 (MQ=255)
gATGGTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGcctc > 1:2561591/1‑71 (MQ=255)
gATGGTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGcctc > 1:2521137/1‑71 (MQ=255)
gATGGTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGcctc > 1:1458848/1‑71 (MQ=255)
gATGGTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGcctc < 1:1156877/71‑1 (MQ=255)
gATGGTCGCCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGcctc > 1:2449562/1‑71 (MQ=255)
gATGGTCGCCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGcctc > 1:2198453/1‑71 (MQ=255)
ggTCGTCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGcctcct > 1:110042/1‑70 (MQ=255)
|
TCTTCAGTGAGCTGACGGAACTGTTGTTCCTGTGCTTCATCTTTAAACTGCAACACATCGATGGTCGCCAGCGCTGAGCCGGAGATCATCAGCATCAGCACGCCCAATAAAAACCTCATTGTGCGGCCTCCT > W3110S.gb/2295626‑2295757
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
