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 |
1,202,265 |
G→T |
34.1% |
A40D (GCT→GAT) |
intE ← |
predicted integrase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,202,265 | 0 | G | T | 34.1%
| 70.1
/ 26.2
| 41 | A40D (GCT→GAT) | intE | predicted integrase |
| Reads supporting (aligned to +/- strand): ref base G (10/17); new base T (9/5); total (19/22) |
| Fisher's exact test for biased strand distribution p-value = 1.15e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.88e-01 |
CTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTAC > W3110S.gb/1202196‑1202325
|
cTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAg > 1:1524681/1‑70 (MQ=255)
gCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAAttt < 1:1292059/71‑1 (MQ=255)
gCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAAttt < 1:365969/71‑1 (MQ=255)
ccAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAAtttt < 1:2107815/71‑1 (MQ=255)
gCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTg > 1:1999414/1‑71 (MQ=255)
tgtTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAAtttt < 1:1172317/62‑1 (MQ=255)
ttGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAATCATGGAATTTTCCTGTCa > 1:2678215/1‑67 (MQ=255)
ttGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTg < 1:1720965/70‑1 (MQ=255)
ttGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTg < 1:1815358/70‑1 (MQ=255)
ttGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTg < 1:747217/70‑1 (MQ=255)
ggCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTGGAt > 1:185190/1‑71 (MQ=255)
ggCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGa < 1:741772/70‑1 (MQ=255)
cTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCt < 1:1001635/71‑1 (MQ=255)
gTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGaa < 1:484313/47‑1 (MQ=255)
gTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTtat < 1:673507/70‑1 (MQ=255)
tGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAATCATGGAATTTTc < 1:831338/51‑1 (MQ=255)
ggCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTGGATGCTTATAcc > 1:1027065/1‑71 (MQ=255)
ggCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTGGATGCTTATAc > 1:179688/1‑70 (MQ=255)
gCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCa > 1:1515712/1‑39 (MQ=255)
aTAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGcc > 1:648287/1‑70 (MQ=255)
tAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAAtttt < 1:1258289/44‑1 (MQ=255)
tAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTtat < 1:281020/63‑1 (MQ=255)
aGCGATAGCTTCAGCTTCGTTTGTTCCCAAATCATGGAATTTTCCTGTCAc > 1:1458430/1‑51 (MQ=255)
aGCGATAGCTTCAGCTTCGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTGGATGCTta > 1:729770/1‑61 (MQ=255)
aGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCaa > 1:218646/1‑70 (MQ=255)
gCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCaa > 1:1201671/1‑69 (MQ=255)
gATAGCTTCAGCTTCGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTGGa > 1:369599/1‑52 (MQ=255)
tAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACt > 1:2265989/1‑71 (MQ=255)
gcttcagcttcGTTTGTTCCCAAAGCATGGAAtttt < 1:557971/36‑1 (MQ=255)
gcttcagcttcGTTTGTTCCCAAAGCATGGAATTTTCCTGTCa > 1:1058241/1‑43 (MQ=255)
gcttcagcttcGTTTGTTCCCAAAGCATGGAATTTTCCTGTCa > 1:2189763/1‑43 (MQ=255)
gcttcagcttcGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACttt < 1:2470332/71‑1 (MQ=255)
agcttcGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACtttattta > 1:2702657/1‑71 (MQ=255)
agcttcGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACtttattt < 1:1237699/70‑1 (MQ=255)
agcttcGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACtttattta < 1:2682511/71‑1 (MQ=255)
agcttcGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACtttattta < 1:2421330/71‑1 (MQ=255)
ttcGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCt > 1:1882302/1‑71 (MQ=255)
tcGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGc > 1:2646530/1‑51 (MQ=255)
cGTTTGTTCCCAAATCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCt < 1:2592421/69‑1 (MQ=255)
cGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCt < 1:175363/69‑1 (MQ=255)
tttGTTCCCAAATCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACtttattt < 1:1304866/63‑1 (MQ=255)
tGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCctac > 1:2152879/1‑71 (MQ=255)
|
CTTTGTTCAGCCAGGCGAGTGTTGGCCTCAGTGGCAATAGCGATAGCTTCAGCTTCGTTTGTTCCCAAAGCATGGAATTTTCCTGTCACTGGATGCTTATACCGCCAATAGACTTTATTTACCTTCCTAC > W3110S.gb/1202196‑1202325
|
| 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
