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 I177 R1
|
141 |
27.5 |
996908 |
97.7% |
973979 |
124.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
966,040 |
A→G |
D399G (GAT→GGT) |
ycaQ → |
winged helix DNA‑binding protein YcaQ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 966,040 | 0 | A | G | 100.0%
| 51.3
/ NA
| 15 | D399G (GAT→GGT) | ycaQ | winged helix DNA‑binding protein YcaQ |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (7/8); total (7/8) |
CAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTG > NZ_CP009273/965916‑966156
|
cAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCt > 2:36255/1‑139 (MQ=255)
ggTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGaaa > 2:883/1‑139 (MQ=255)
ccAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCg < 2:158786/139‑1 (MQ=255)
cGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAAt > 2:249067/1‑139 (MQ=255)
aaGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGAt < 2:492840/139‑1 (MQ=255)
tACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGAtt > 2:217259/1‑139 (MQ=255)
tCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATg < 1:428756/139‑1 (MQ=255)
tCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATg < 2:127666/139‑1 (MQ=255)
cGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGa > 1:193977/1‑135 (MQ=255)
cGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGa < 2:193977/135‑1 (MQ=255)
aCTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTgg < 1:883/139‑1 (MQ=255)
tcagcagGCAACGCGGGTGACATTAGGATGCTGCCCGTAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTggag < 1:202896/136‑1 (MQ=255)
gcagcaGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTggag < 1:249067/137‑1 (MQ=255)
aCGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCCTCTGGAGGAACTATGGat > 1:236118/1‑138 (MQ=255)
tgcCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATtg > 1:266331/1‑139 (MQ=255)
|
CAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTG > NZ_CP009273/965916‑966156
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 36 ≤ 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
TCCTTGAAGTTATCTCTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAAACTT > NZ_CP009273/965890‑966182
|
TCCTTGAAGTTATCTCTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGG > SRR3722131.160614/1‑151 (MQ=60)
TCCTTGAAGTTATCTCTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGG > SRR3722131.498105/1‑151 (MQ=60)
GTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACC < SRR3722131.433389/151‑1 (MQ=60)
ATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCAT > SRR3722131.196205/1‑151 (MQ=60)
AACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGG < SRR3722131.888/151‑1 (MQ=60)
GTCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGTAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGAT < SRR3722131.205256/149‑1 (MQ=60)
GGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCCTCTGGAGGAACTATGGATC > SRR3722131.238917/1‑150 (MQ=60)
GGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGAT < SRR3722131.251992/149‑1 (MQ=60)
CATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGC > SRR3722131.269439/1‑151 (MQ=60)
agCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAAAC < SRR3722131.477746/149‑1 (MQ=60)
CTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAAACTT > SRR3722131.35754/1‑151 (MQ=60)
|
TCCTTGAAGTTATCTCTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAAACTT > NZ_CP009273/965890‑966182
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
