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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,465,710 |
G→A |
28.8% |
A421A (GCC→GCT) |
gyrA ← |
DNA gyrase (type II topoisomerase), subunit A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,465,710 | 0 | G | A | 28.8%
| 36.2
/ 12.9
| 38 | A421A (GCC→GCT) | gyrA | DNA gyrase (type II topoisomerase), subunit A |
| Reads supporting (aligned to +/- strand): ref base G (19/8); new base A (5/6); total (24/14) |
| Fisher's exact test for biased strand distribution p-value = 2.66e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01 |
GCCGAACTCTGGCTCCAGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATG > minE/1465647‑1465778
|
gcCGAACTCTGGCTCCAGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAAc < 1:678414/69‑1 (MQ=255)
gcCGAACTCTGGCTCCAGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAAc < 1:2527330/69‑1 (MQ=255)
gcCGAACTCTGGCTCCAGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAAc < 1:179873/69‑1 (MQ=255)
tCCAGCCATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGc < 1:2790928/66‑1 (MQ=255)
tCCAGCCATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGc < 1:2413676/66‑1 (MQ=255)
tCCAGCCATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGc < 1:1344327/66‑1 (MQ=255)
tCCAGCCATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGc < 1:3415502/66‑1 (MQ=255)
ccAGCCATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGc < 1:256772/65‑1 (MQ=255)
ccATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGCTGCCACgg > 1:3168276/1‑69 (MQ=255)
ccATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGCTGCCACgg > 1:2351103/1‑69 (MQ=255)
ccATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGCTGCCACgg > 1:2016210/1‑69 (MQ=255)
ccATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGCTGCCACgg > 1:3116026/1‑69 (MQ=255)
ccATTCCGGACGCGCAGCATCGTCGCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGCTGCCACgg > 1:561290/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACgg > 1:487899/1‑66 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:2211912/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:877380/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:2640952/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:2640429/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:1099653/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:615799/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:1319348/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:2951788/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:1565431/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:3099136/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:1991853/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:392579/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:3379064/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:1608364/1‑69 (MQ=255)
ttCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGAtt > 1:1579344/1‑69 (MQ=255)
ccGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTa > 1:1057632/1‑68 (MQ=255)
ccGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTa > 1:239353/1‑68 (MQ=255)
ccGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTa > 1:1503507/1‑68 (MQ=255)
tcgtcgCCCGCACGTTCCAGCATCGCAGCAACGTTGCCCAGc < 1:1020575/42‑1 (MQ=37)
gCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGc < 1:168240/69‑1 (MQ=255)
tCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCa < 1:928590/66‑1 (MQ=255)
tCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCa < 1:1792059/66‑1 (MQ=255)
tCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCa < 1:69815/66‑1 (MQ=255)
tCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCa < 1:1380744/66‑1 (MQ=255)
gcgGCAACGTTGCCCCGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGgcgc > 1:1191270/1‑68 (MQ=255)
gcgGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGgcgc > 1:1447491/1‑68 (MQ=255)
gcgGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGgcgc > 1:2749520/1‑68 (MQ=255)
gcgGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGgcgc > 1:1472347/1‑68 (MQ=255)
gcgGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGgcgc > 1:2070528/1‑68 (MQ=255)
gcgGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGACGgcgc > 1:141848/1‑68 (MQ=255)
ggCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCAt < 1:2692725/68‑1 (MQ=255)
ggCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATg < 1:1232845/69‑1 (MQ=255)
ggCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATg < 1:3225824/69‑1 (MQ=255)
ggCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATg < 1:717111/69‑1 (MQ=255)
|
GCCGAACTCTGGCTCCAGCCATTCCGGACGCGCAGCATCGTCGCCAGCACGTTCGAGCATCGCGGCAACGTTGCCCAGCTGCCACGGATTAGCAACCAGCGCAGTTTTCGCTTCTGCAGGCGTCGGCGCATG > minE/1465647‑1465778
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
