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 F5 I184 R1
|
278 |
29.6 |
1166432 |
97.3% |
1134938 |
124.1 |
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%
| 94.7
/ NA
| 28 | 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 (14/14); total (14/14) |
CCAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAAC > NZ_CP009273/678784‑679046
|
ccAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATc > 2:350868/1‑138 (MQ=255)
cAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACgtg > 2:51364/1‑139 (MQ=255)
acggCGAGTTCTGGATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTACAGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGCAAAATTTCAGCCGATCAGCCAGTa > 2:366216/3‑138 (MQ=255)
aTGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTa > 2:52328/1‑138 (MQ=255)
aGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaa > 2:6965/1‑138 (MQ=255)
gTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaaca < 2:60458/139‑1 (MQ=255)
ttCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaaca > 2:547062/1‑138 (MQ=255)
cATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGccc < 2:205149/139‑1 (MQ=255)
ttATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTg < 1:51364/139‑1 (MQ=255)
ttATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTg < 2:243294/139‑1 (MQ=255)
tCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGAc > 2:569615/1‑138 (MQ=255)
tttATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATc < 1:547062/139‑1 (MQ=255)
atatCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGa < 1:6965/138‑1 (MQ=255)
tatCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGAc < 1:169496/138‑1 (MQ=255)
ttGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTa > 2:461365/1‑139 (MQ=255)
tGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTAc > 2:523311/1‑139 (MQ=255)
gaaagaaaAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTa < 1:52328/137‑1 (MQ=255)
aaGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCAtt < 2:540428/139‑1 (MQ=255)
aTTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGAc > 1:490412/1‑111 (MQ=255)
aTTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGAc < 2:490412/111‑1 (MQ=255)
aGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCa < 1:461365/139‑1 (MQ=255)
accaccCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGa < 1:240252/139‑1 (MQ=255)
cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCCGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCAt > 1:260990/1‑115 (MQ=255)
cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCGTTCGGTTTATTGCCTGTCAGataa > 2:54454/1‑138 (MQ=255)
cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCAt < 2:260990/115‑1 (MQ=255)
cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGataa > 2:56393/1‑138 (MQ=255)
cccAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGataa > 1:263201/1‑138 (MQ=255)
gtggtgGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATcaacaa < 2:263201/139‑1 (MQ=255)
tggtggTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCaacaac > 2:18908/1‑139 (MQ=255)
|
CCAGACGGCAATTAAACTATTGGTAGTACCGAGATCGATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAAC > NZ_CP009273/678784‑679046
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCGTCATACCCTGGG > NZ_CP009273/678841‑679060
|
gggctcggaaatgtgtataagagacagGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACAT < SRR3722139.60604/124‑1 (MQ=60)
ATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACAT < SRR3722139.51950/151‑1 (MQ=60)
ATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGG < SRR3722139.553352/151‑1 (MQ=60)
TATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTG < SRR3722139.7033/150‑1 (MQ=60)
ATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGG < SRR3722139.171618/150‑1 (MQ=60)
TGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTC < SRR3722139.52925/149‑1 (MQ=60)
GAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCtgtctcttatacacatc > SRR3722139.496102/1‑134 (MQ=60)
GATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCCGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCtgtctcttatac > SRR3722139.264270/1‑138 (MQ=60)
GATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAAT > SRR3722139.266503/1‑150 (MQ=60)
AAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAA < SRR3722139.466767/151‑1 (MQ=60)
GACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATC < SRR3722139.243227/151‑1 (MQ=60)
GTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCGTCATACCCTGGG < SRR3722139.185644/151‑1 (MQ=60)
|
ATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATTCGGTTTATTGCCTGTCAGATAATAATAATCAACAACCGTCATACCCTGGG > NZ_CP009273/678841‑679060
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
