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 |
2,713,857 |
A→G |
70.3% |
G168G (GGT→GGC) |
nirB ← |
nitrite reductase, large subunit, NAD(P)H‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,713,857 | 0 | A | G | 70.3%
| 64.9
/ 28.4
| 67 | G168G (GGT→GGC) | nirB | nitrite reductase, large subunit, NAD(P)H‑binding |
| Reads supporting (aligned to +/- strand): ref base A (17/3); new base G (32/15); total (49/18) |
| Fisher's exact test for biased strand distribution p-value = 2.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
TCTGATCAAGCTGTTCTGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGACCTAACAGGCCGCCACCAACAAC > minE/2713799‑2713913
|
tCTGATCATGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:941894/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCTATAACGTGGGTTTCAATGCCTAAGtttt < 1:1732068/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:1029698/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:51757/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:643411/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:2500807/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:2504895/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:467129/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:2655035/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:420311/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:143630/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:2947876/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:810625/69‑1 (MQ=255)
tCTGATCAAGCTGTTCCGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:1276991/69‑1 (MQ=255)
ggATCAAGCTGTTCTGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTc > 1:3144684/2‑69 (MQ=255)
cAAGCTGTTCTGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAgcg > 1:134197/1‑69 (MQ=255)
aaGCTGTTCTGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAgcgc < 1:1388164/69‑1 (MQ=255)
gCTGTTCTGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAgcgcgc > 1:1790747/1‑69 (MQ=255)
gCTGTTCTGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAgcgcgc > 1:554610/1‑69 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGt > 1:1967383/1‑46 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:2900541/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:2896753/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:3428098/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:2587097/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:3348111/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:3249367/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:3325985/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:2363256/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:633664/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:1753387/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:716413/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:750230/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:1674955/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:1578286/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:789086/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:146784/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:1389400/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:1359017/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:1358684/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:1232171/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:116074/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCt > 1:1132860/1‑66 (MQ=255)
aTCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTc < 1:1034417/68‑1 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAg > 1:762745/1‑68 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa > 1:615346/1‑69 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa > 1:1347914/1‑69 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa < 1:1684694/69‑1 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa > 1:646858/1‑69 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa > 1:3108472/1‑69 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa > 1:2346906/1‑69 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa > 1:2548925/1‑69 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa > 1:2761297/1‑69 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa > 1:2995776/1‑69 (MQ=255)
aGCATAGGGGCAAATTCGATAACGTGGGTTTCAATAACTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGa > 1:968745/1‑69 (MQ=255)
ggggCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGACCTAAc > 1:2413211/1‑69 (MQ=255)
ggggCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGACCTAAc > 1:495687/1‑69 (MQ=255)
ggggCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGACCTAAc > 1:2048257/1‑69 (MQ=255)
gCAAATTCGATAACGTGGGTTTCAATGCCTAAGtttt < 1:726420/37‑1 (MQ=255)
tGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCTTCCAGACCTAACAGGCCGCCACCaacaac > 1:64643/1‑68 (MQ=255)
tGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCTTCCAGACCTAACAGGCCGCCACCaacaac > 1:1082411/1‑68 (MQ=255)
tGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCTTCCAGACCTAACAGGCCGCCACCaacaac > 1:890926/1‑68 (MQ=255)
tGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCTTCCAGACCTAACAGGCCGCCACCaacaac > 1:989624/1‑68 (MQ=255)
tGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCTTCCAGACCTAACAGGCCGCCACCaacaac > 1:1531466/1‑68 (MQ=255)
tGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCTTCCAGACCTAACAGGCCGCCACCaacaac > 1:1679080/1‑68 (MQ=255)
tGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCTTCCAGACCTAACAGGCCGCCACCaacaac > 1:2171836/1‑68 (MQ=255)
tGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCTTCCAGACCTAACAGGCCGCCACCaacaac > 1:483802/1‑68 (MQ=255)
tGGGTTTCAATGCCTAAGTTTTTCAGCGCGCCAGCAGCTTCCAGACCTAACAGGCCGCCACCaacaac > 1:3358029/1‑68 (MQ=255)
|
TCTGATCAAGCTGTTCTGCCATCAGCATAGGGGCAAATTCGATAACGTGGGTTTCAATACCTAAGTTTTTCAGCGCGCCTGCGGCTTCCAGACCTAACAGGCCGCCACCAACAAC > minE/2713799‑2713913
|
| 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
