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 I2 R1
|
764 |
42.0 |
2018750 |
95.5% |
1927906 |
109.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,567,249 |
C→T |
intergenic (‑3/+38) |
yjiN ← / ← mdtM |
zinc‑type alcohol dehydrogenase‑like protein/multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,567,249 | 0 | C | T | 96.0%
| 70.7
/ ‑3.8
| 25 | intergenic (‑3/+38) | yjiN/mdtM | zinc‑type alcohol dehydrogenase‑like protein/multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (11/13); total (11/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.17e-01 |
CAGCAATCGCCTTCACGCCGCTCACCCAAAAATTGGGCGGCAAAAACAGCGTAACGACAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAACGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAACGACGATAACGCCCGCCAC > NC_000913/4567114‑4567376
|
cAGCAATCGCCTTCACGCCGCTCACCCAAAAATTGGGCGGCAAAAACAGCGTAACGACAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGtt < 2:688784/139‑1 (MQ=255)
aGCAATCGCCTTCACGCCGCTCACCCAAAAATTGGGCGGCAAAAACAGCGTAACGACAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTa < 1:112356/139‑1 (MQ=255)
cACGCCGCTCACCCAAAAATTGGGCGGCAAAAACAGCGTAACGACAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCt < 2:755060/139‑1 (MQ=255)
ggcggcAAAAACAGCGTAACGACAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGtt < 1:174189/104‑1 (MQ=255)
ggcggcAAAAACAGCGTAACGACAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGtt > 2:174189/1‑104 (MQ=255)
aaaCAGCGTAACGACAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAACGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGctc < 1:207893/139‑1 (MQ=255)
cGACAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCt > 1:471439/1‑139 (MQ=255)
cAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCgg < 2:471439/139‑1 (MQ=255)
gcagcGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGa > 1:802763/1‑139 (MQ=255)
ggcgATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTg > 1:88296/1‑139 (MQ=255)
tAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCa < 2:88296/139‑1 (MQ=255)
gCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCAcgc < 2:252080/139‑1 (MQ=255)
agagCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCt < 1:897777/65‑1 (MQ=255)
agagCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCt > 2:897777/1‑65 (MQ=255)
gcgcCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCt < 2:820073/62‑1 (MQ=255)
gcgcCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCt > 1:820073/1‑62 (MQ=255)
gcgcCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATc > 2:687155/1‑139 (MQ=255)
aCCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCa < 2:112721/139‑1 (MQ=255)
ttttGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCt > 1:918020/1‑53 (MQ=255)
ttttGGCGCGTCTGAGTTCGATGAGTTTATTCATAATGTTAAGAATAGAGCCt < 2:918020/53‑1 (MQ=255)
tGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAg > 2:411487/1‑71 (MQ=255)
tGAGTTTATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAg < 1:411487/71‑1 (MQ=255)
tttATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCATTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCa > 2:682059/1‑90 (MQ=255)
tttATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCa < 1:682059/90‑1 (MQ=255)
tttATTCATAATGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAACGACGATAACGCCCGCcac > 2:110326/1‑139 (MQ=255)
|
CAGCAATCGCCTTCACGCCGCTCACCCAAAAATTGGGCGGCAAAAACAGCGTAACGACAAAGGTAGCAGCGGCGATAAGCAGTAAAGAGAGCGCCAACCTTTTGGCGCGTCTGAGTTCGATGAGTTTATTCATAACGTTAAGAATAGAGCCTGACGGCCGGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAACGACGATAACGCCCGCCAC > NC_000913/4567114‑4567376
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
