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 |
|
A1 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
678,913 |
A→G |
intergenic (‑64/+20) |
hscC ← / ← rihA |
molecular chaperone HscC/pyrimidine‑specific ribonucleoside hydrolase RihA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 678,913 | 0 | A | G | 100.0%
| 138.5
/ NA
| 37 | intergenic (‑64/+20) | hscC/rihA | molecular chaperone HscC/pyrimidine‑specific ribonucleoside hydrolase RihA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (22/15); total (22/15) |
AATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCAT > NZ_CP009273/678826‑678998
|
aaTGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCt < 1:1065240/91‑1 (MQ=255)
aaTGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCt < 1:795549/91‑1 (MQ=255)
tGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTa < 1:255239/91‑1 (MQ=255)
ggCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTaa > 1:552437/1‑91 (MQ=255)
aGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCaa < 2:64055/91‑1 (MQ=255)
ttCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATg < 2:871555/91‑1 (MQ=255)
aTCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGtt > 1:515273/1‑91 (MQ=255)
ttGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCg > 1:464624/1‑91 (MQ=255)
ttGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCg > 2:1110183/1‑91 (MQ=255)
ttGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCg > 2:1042295/1‑91 (MQ=255)
ttATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAAt > 2:134186/1‑91 (MQ=255)
cTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGa > 2:326016/1‑91 (MQ=255)
ttGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGAc > 2:499385/1‑91 (MQ=255)
aaaGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCa < 2:552437/91‑1 (MQ=255)
agagATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGTTCAGCCAGt < 1:1067038/91‑1 (MQ=255)
aaaCAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATca > 1:21801/1‑91 (MQ=255)
aGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaacaa < 1:803012/91‑1 (MQ=255)
aGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaacaa < 1:1015820/91‑1 (MQ=255)
gATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACaaa > 2:439015/1‑91 (MQ=255)
aGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCt < 2:1097461/91‑1 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAAtt < 1:55729/53‑1 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAAtt > 2:55729/1‑53 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGa > 2:991977/1‑88 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGa < 1:991977/88‑1 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 2:429409/1‑91 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 2:1101854/1‑91 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 2:642549/1‑91 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 2:818498/1‑91 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 2:964516/1‑91 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGAAAATCAACAAAGCCATGAcaa > 2:580470/1‑89 (MQ=255)
ggTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAAc > 2:577657/1‑91 (MQ=255)
tAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACAt < 1:134186/91‑1 (MQ=255)
aCGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCg < 1:499385/91‑1 (MQ=255)
aCGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCg > 1:197541/1‑91 (MQ=255)
cgcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAg > 1:57807/1‑55 (MQ=255)
cgcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAg < 2:57807/55‑1 (MQ=255)
gcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAACGCCCTGACGATCAACATCGAc > 2:612166/1‑91 (MQ=255)
tggtggTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCAt > 1:370870/1‑91 (MQ=255)
tggtggTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCAt > 2:898318/1‑91 (MQ=255)
|
AATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCAT > NZ_CP009273/678826‑678998
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGG > NZ_CP009273/678818‑679013
|
TCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTA < SRR3722125.403939/101‑1 (MQ=60)
CGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAA > SRR3722125.564278/1‑101 (MQ=60)
ATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATC < SRR3722125.369575/101‑1 (MQ=60)
ATACCAACGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAATAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATC < SRR3722125.1099564/101‑1 (MQ=60)
AATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGA < SRR3722125.1089224/101‑1 (MQ=60)
AATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGA < SRR3722125.812914/101‑1 (MQ=60)
TGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACG < SRR3722125.260386/101‑1 (MQ=60)
GTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTT > SRR3722125.526214/1‑101 (MQ=60)
GCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCG > SRR3722125.474421/1‑101 (MQ=60)
CATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGctgtctcttatac > SRR3722125.409525/1‑88 (MQ=60)
tgggctcggagatgtgtataagagacagGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATC < SRR3722125.56751/73‑1 (MQ=60)
AAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCA > SRR3722125.22192/1‑101 (MQ=60)
AGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGTTCAGCCAGTAAATCAACAA < SRR3722125.1091064/101‑1 (MQ=60)
AGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACG < SRR3722125.1038545/101‑1 (MQ=60)
AGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACG < SRR3722125.820566/101‑1 (MQ=60)
AGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTActgtctcttatacacatctccgagcccacgagactaggcatgatctcgtatgcc > SRR3722125.303495/1‑47 (MQ=60)
ACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACAT < SRR3722125.1014127/101‑1 (MQ=60)
CACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCG > SRR3722125.201436/1‑101 (MQ=60)
ACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCctgtctcttatacacatctccgagcc > SRR3722125.58866/1‑75 (MQ=60)
AGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCAT > SRR3722125.378637/1‑101 (MQ=60)
TAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTAC < SRR3722125.136733/101‑1 (MQ=60)
ACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGG < SRR3722125.509951/101‑1 (MQ=60)
GTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGG > SRR3722125.468968/1‑101 (MQ=60)
|
TCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGG > NZ_CP009273/678818‑679013
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
