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 |
|
A3 F50 I2 R1
|
193 |
39.9 |
1341687 |
91.8% |
1231668 |
149.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,594,132 |
(C)8→9 |
pseudogene (3856/3861 nt) |
yneO ← |
pseudogene, AidA homolog |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,594,124 | 1 | . | C | 96.0%
| 85.2
/ ‑3.8
| 25 | pseudogene (2/1461 nt) | yneO | pseudogene, AidA homolog |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (15/9); total (15/10) |
| Fisher's exact test for biased strand distribution p-value = 4.00e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
GAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGATAT > NC_000913/1593985‑1594263
|
gAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑cccc‑ccccca < 2:584625/150‑3 (MQ=255)
tctttCCGGTATATTTGCCGTTAACGGTCAGTACTTTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCTTTCCGCCATTCTCCAGGTTCCCGCCCTTATTGGGTTTAGGGACCCGCAGTG‑CCCCACCCCAGGCATAACGTTCata < 1:6173/146‑1 (MQ=255)
tttCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCAcc > 2:4726/1‑151 (MQ=255)
ggTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGc > 2:478350/1‑149 (MQ=255)
gTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAgt > 1:45235/1‑151 (MQ=255)
gTATAGTGGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGTTTGCCGCCGATAGTGGTTTTAGCGGCACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCa < 2:184791/149‑1 (MQ=255)
aGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAgtggt < 1:498874/150‑1 (MQ=255)
aaCGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCg > 2:107005/1‑151 (MQ=255)
ggTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGa < 1:344459/139‑1 (MQ=255)
ggTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGa > 2:344462/1‑139 (MQ=255)
aGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATcac > 2:661230/1‑151 (MQ=255)
tACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac > 2:534700/1‑151 (MQ=255)
cATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTTGTGACATTTCCCGACATCACAcc < 1:599062/150‑1 (MQ=255)
aTTCCCCGGTTTCCCCCCTTCGCTATTCTTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGc > 1:479711/1‑151 (MQ=255)
ccccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTg < 2:204523/150‑1 (MQ=255)
cccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt < 2:602372/151‑1 (MQ=255)
ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGatat > 2:250412/1‑151 (MQ=255)
ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGatat < 1:317762/151‑1 (MQ=255)
tCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACtt > 1:600501/1‑151 (MQ=255)
aTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGc < 2:64918/151‑1 (MQ=255)
gAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCat > 2:327427/1‑150 (MQ=255)
ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATAtt > 2:490391/1‑150 (MQ=255)
tctcCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCg > 1:550319/1‑151 (MQ=255)
gccgccGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAg < 2:131529/151‑1 (MQ=255)
cgATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAAtt > 1:542617/1‑151 (MQ=255)
gACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGatat > 2:589809/1‑151 (MQ=255)
|
GAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGATAT > NC_000913/1593985‑1594263
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
