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 F3 I0 R1
|
328 |
90.1 |
2317887 |
85.2% |
1974839 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,787,031 |
C→T |
100% |
A140A (GCG→GCA) |
yfjG ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,787,031 | 0 | C | T | 81.4%
| 151.9
/ 27.2
| 70 | A140A (GCG→GCA) | yfjG | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (7/6); new base T (0/57); total (7/63) |
| Fisher's exact test for biased strand distribution p-value = 1.43e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ACTGTAAACCTCTTTCGCACGAACCGTAAAAGCCTGGACCATATTAGCCGCCAGCTCTTTAAACACGCGACCAAAGG > minE/1786983‑1787059
|
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTTAacac < 1:1539538/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTTAacac < 1:514262/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:325125/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1793650/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1863808/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:192549/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1958119/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1960269/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:2047416/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:213048/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:2137488/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:2222503/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:2277790/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:228116/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:239547/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:264746/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:2003298/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:422124/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:442011/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:546050/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:54963/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:569194/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:59215/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:61962/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:740977/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:800906/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:921180/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:992544/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:999673/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1752231/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1026454/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1035251/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1041797/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1049534/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1148543/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1241939/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1247767/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1276729/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1318054/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1353431/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1378289/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1408853/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:14653/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1469220/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1610255/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1777185/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1747280/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1713120/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1482070/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1555554/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1539341/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1489793/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCACCTCTTTAAacac < 1:2158393/66‑1 (MQ=255)
aCTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCACCTCTTTAAacac < 1:2155498/66‑1 (MQ=255)
aCTGTAGACCTCTCTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:2040644/66‑1 (MQ=255)
aCTGTAGACCTATTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:563342/66‑1 (MQ=255)
cTGTAGACCTCTTTTGCACGAACAGTAAAAGCCTGCACCATATTAGCTGCCAGCTCTTTAAacac < 1:1673092/65‑1 (MQ=255)
ctTTCGCACGAACCGTAAAAGCCTGGACCATATTAGCCGCCAGctc > 1:1384653/1‑46 (MQ=255)
ctTTCGCACGAACCGTAAAAGCCTGGACCATATTAGCCGCCAGctc > 1:32106/1‑46 (MQ=255)
ctTTCGCACGAACCGTAAAAGCCTGGACCATATTAGCCGCCAGctc > 1:52638/1‑46 (MQ=255)
ctTTCGCACGAACCGTAAAAGCCTGGACCATATTAGCCGCCAGctc > 1:544501/1‑46 (MQ=255)
ctTTCGCACGAACCGTAAAAGCCTGGACCATATTAGCCGCCAGctc > 1:1279417/1‑46 (MQ=255)
ctTTCGCACGAACCGTAAAAGCCTGGACCATATTAGCCGCCAGctc > 1:2292818/1‑46 (MQ=255)
ctTTCGCACGAACCGTAAAAGCCTGGACCATATTAGCCGCCAGctc > 1:1038116/1‑46 (MQ=255)
aaaGCCTGGACCATATTAGCCGCCAGCTCTTTAAACACGCGACCAAAgg < 1:2284936/49‑1 (MQ=255)
aaaGCCTGGACCATATTAGCCGCCAGCTCTTTAAACACGCGACCAAAgg < 1:904602/49‑1 (MQ=255)
aaaGCCTGGACCATATTAGCCGCCAGCTCTTTAAACACGCGACCAAAgg < 1:663258/49‑1 (MQ=255)
aaaGCCTGGACCATATTAGCCGCCAGCTCTTTAAACACGCGACCAAAgg < 1:633377/49‑1 (MQ=255)
aaaGCCTGGACCATATTAGCCGCCAGCTCTTTAAACACGCGACCAAAgg < 1:1665538/49‑1 (MQ=255)
aaaGCCTGGACCATATTAGCCGCCAGCTCTTTAAACACGCGACCAAAgg < 1:1011148/49‑1 (MQ=255)
|
ACTGTAAACCTCTTTCGCACGAACCGTAAAAGCCTGGACCATATTAGCCGCCAGCTCTTTAAACACGCGACCAAAGG > minE/1786983‑1787059
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
