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 |
1,996,903 |
G→A |
23.1% |
G119G (GGG→GGA) |
yqgA → |
predicted inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,996,903 | 0 | G | A | 23.1%
| 53.5
/ 10.3
| 43 | G119G (GGG→GGA) | yqgA | predicted inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (22/11); new base A (5/5); total (27/16) |
| Fisher's exact test for biased strand distribution p-value = 4.60e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01 |
AATCTTTTATTCAGAATTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTCTT > minE/1996845‑1996969
|
aaTCTTTTATTCAGAATTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCggg > 1:1658422/1‑68 (MQ=255)
aaTCTTTTATTCAGAATTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCggg > 1:842177/1‑68 (MQ=255)
aaTTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAgg < 1:996867/68‑1 (MQ=255)
aaTTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAgg < 1:3155885/68‑1 (MQ=255)
aaTTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAgg < 1:243858/68‑1 (MQ=255)
aaTTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAgg < 1:83313/68‑1 (MQ=255)
tATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATg < 1:1954862/69‑1 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTc > 1:863328/1‑47 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACgca > 1:3232197/1‑60 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACTAAGGGATGa > 1:3084534/1‑69 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGa > 1:1407017/1‑61 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGa > 1:2845020/1‑61 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATg > 1:2554072/1‑68 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGa > 1:2141963/1‑69 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGa > 1:1187003/1‑69 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGa > 1:3366417/1‑69 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGa > 1:2622457/1‑69 (MQ=255)
aTGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGa > 1:1740062/1‑69 (MQ=255)
tattGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTc > 1:125179/1‑37 (MQ=255)
tattGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAgg > 1:2624091/1‑54 (MQ=255)
tattGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAgg > 1:29092/1‑54 (MQ=255)
tattGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAgg > 1:3249944/1‑54 (MQ=255)
gTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGt < 1:2308055/69‑1 (MQ=255)
gTTTTGCGCCAGCGGCACCGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTAtttt > 1:691998/1‑69 (MQ=255)
gTTTTGCGCCAGCGGCACCGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTAtttt > 1:2688038/1‑69 (MQ=255)
gTTTTGCGCCAGCGGCACCGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTAtttt > 1:2737996/1‑69 (MQ=255)
gTTTTGCGCCAGCGGCACCGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTAtttt > 1:1738392/1‑69 (MQ=255)
gTTTTGCGCCAGCGGCACCGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTAtttt > 1:3149645/1‑69 (MQ=255)
ttGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAgg < 1:312370/42‑1 (MQ=255)
ttGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGa > 1:726724/1‑47 (MQ=255)
ttGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTa < 1:139190/67‑1 (MQ=255)
ttGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTa < 1:3041551/67‑1 (MQ=255)
ttGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTa < 1:3178936/67‑1 (MQ=255)
ttGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAAt > 1:2642780/1‑69 (MQ=255)
ttGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAAt > 1:2575028/1‑69 (MQ=255)
ttGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAAt > 1:2412978/1‑69 (MQ=255)
ttGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAAt > 1:1549245/1‑69 (MQ=255)
cAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTa < 1:2535285/61‑1 (MQ=255)
ccGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTc < 1:2961195/69‑1 (MQ=255)
ccGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTc < 1:2816883/69‑1 (MQ=255)
ccGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTc < 1:1003556/69‑1 (MQ=255)
ccGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTc < 1:1408267/69‑1 (MQ=255)
ccGGAATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTc < 1:1111646/69‑1 (MQ=255)
gggATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTCtt > 1:135393/1‑69 (MQ=255)
|
AATCTTTTATTCAGAATTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTCTT > minE/1996845‑1996969
|
| 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
