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 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,938,519 |
A→G |
17.0% |
I166V (ATC→GTC) |
fucR → |
DNA‑binding transcriptional activator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,938,519 | 0 | A | G | 17.0%
| 125.9
/ 19.7
| 53 | I166V (ATC→GTC) | fucR | DNA‑binding transcriptional activator |
| Reads supporting (aligned to +/- strand): ref base A (20/24); new base G (5/4); total (25/28) |
| Fisher's exact test for biased strand distribution p-value = 7.19e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01 |
ACACTTGAGCGCAAATATGGCTGTTACGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAGCGGCGCACTGTGGGACTCCAATGCG > W3110S.gb/2938453‑2938584
|
acacTTGAGCGCAAATATGGCTGTTACGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAGTCGa < 1:1779327/71‑1 (MQ=255)
acacTTGAGCGCAAATATGGCTGTTACGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAGTCGa < 1:89365/71‑1 (MQ=255)
acacTTGAGCGCAAATATGGCTGTTACGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAGTCGa < 1:55757/71‑1 (MQ=255)
tatGGCTGTTACGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAGTCGa < 1:890237/56‑1 (MQ=255)
tACGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:1159041/1‑71 (MQ=255)
tACGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:1424361/1‑71 (MQ=255)
tACGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:708855/1‑71 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAGTCGATCTGTTTATTTTTTCTTGTGAAgg > 1:298508/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAGTCGATCTGTTTATTTTTTCTTGTGAAgg > 1:430497/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAGTCGATCTGTTTATTTTTTCTTGTGAAgg > 1:1360229/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAGTCGATCTGTTTATTTTTTCTTGTGAAgg > 1:711232/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTAtttt > 1:1454037/1‑58 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:1859329/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:476939/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:478032/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:1447832/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:1211115/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:921971/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:1157786/1‑70 (MQ=255)
aCGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:957635/1‑70 (MQ=255)
aCGTCAATCCCTCGATGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAgg > 1:986601/1‑70 (MQ=255)
cGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAggg < 1:1819565/70‑1 (MQ=255)
tCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATc > 1:963784/1‑71 (MQ=255)
tCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATc < 1:882051/71‑1 (MQ=255)
tCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATc > 1:661370/1‑71 (MQ=255)
tCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATc < 1:1679907/71‑1 (MQ=255)
aTCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTtgtg < 1:1933925/60‑1 (MQ=255)
aTCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTtgtg < 1:1175173/60‑1 (MQ=255)
aTCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTtgtg < 1:614250/60‑1 (MQ=255)
tCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTtgtg < 1:227189/59‑1 (MQ=255)
tCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTtgtg < 1:45543/59‑1 (MQ=255)
tCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTagtg < 1:1492533/59‑1 (MQ=255)
cccTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTtgtg < 1:1741506/58‑1 (MQ=255)
ccTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATag > 1:1892782/1‑70 (MQ=255)
ccTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATag > 1:1374902/1‑70 (MQ=255)
ccTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATag > 1:175186/1‑70 (MQ=255)
ccTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATag > 1:413462/1‑70 (MQ=255)
ccTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATag > 1:38116/1‑70 (MQ=255)
gCTGATTTCCCAACTTAAATCGCTGGAAGTCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAgcg > 1:928790/1‑71 (MQ=255)
aTTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAgcggcg < 1:19970/70‑1 (MQ=255)
aTTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAgcggcg < 1:770510/70‑1 (MQ=255)
aTTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAgcggcg < 1:912372/70‑1 (MQ=255)
aTTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAgcggcg < 1:1344308/70‑1 (MQ=255)
aTTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAgcggcg < 1:1193180/70‑1 (MQ=255)
aaCTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAGCGGCGCACTGTgg < 1:607342/71‑1 (MQ=255)
aCTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAgcggcg < 1:824376/62‑1 (MQ=255)
tCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGTGATCGATAGCAGCGGCGCa < 1:353163/57‑1 (MQ=255)
tCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAGCGGCGCa < 1:1485816/57‑1 (MQ=255)
tCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAGCGGCGCa < 1:1865042/57‑1 (MQ=255)
gAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAGCGGCGCACTGTGGGACTCCAATGCg < 1:496516/69‑1 (MQ=255)
gAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAGCGGCGCACTGTGGGACTCCAATGCg < 1:646903/69‑1 (MQ=255)
gAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAGCGGCGCACTGTGGGACTCCAATGCg < 1:1106459/69‑1 (MQ=255)
gAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAGCGGCGCACTGTGGGACTCCAATGCg < 1:1009485/69‑1 (MQ=255)
|
ACACTTGAGCGCAAATATGGCTGTTACGTCAATCCCTCGCTGATTTCCCAACTTAAATCGCTGGAAATCGATCTGTTTATTTTTTCTTGTGAAGGGATCGATAGCAGCGGCGCACTGTGGGACTCCAATGCG > W3110S.gb/2938453‑2938584
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
