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 I179 R1
|
182 |
40.3 |
1547118 |
96.8% |
1497610 |
120.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
438,112 |
A→G |
S370G (AGC→GGC) |
thiI → |
tRNA 4‑thiouridine(8) synthase ThiI |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 438,112 | 0 | A | G | 100.0%
| 91.1
/ NA
| 25 | S370G (AGC→GGC) | thiI | tRNA 4‑thiouridine(8) synthase ThiI |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (14/11); total (14/11) |
GGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATAT > NZ_CP009273/437985‑438242
|
ggCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGa > 2:346471/1‑138 (MQ=255)
gCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGAt > 2:530896/1‑138 (MQ=255)
cACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGaa < 1:590388/139‑1 (MQ=255)
aaGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGaa < 2:263241/139‑1 (MQ=255)
gCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGa > 1:727435/1‑138 (MQ=255)
ttGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCcag > 1:714118/1‑139 (MQ=255)
ttGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCcag > 1:563906/1‑139 (MQ=255)
tgtgATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAcc > 1:259805/1‑139 (MQ=255)
tgATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAcc > 2:22633/1‑137 (MQ=255)
aTCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAg > 2:328462/1‑138 (MQ=255)
aTCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAg > 1:541463/1‑138 (MQ=255)
aTCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAg < 1:126446/138‑1 (MQ=255)
cAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGa < 1:488004/138‑1 (MQ=255)
cAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGa < 2:27054/138‑1 (MQ=255)
ggTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGgtggaagtg < 1:530896/139‑1 (MQ=255)
ttAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCaa > 1:73461/1‑139 (MQ=255)
aaGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGAGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCg > 1:410003/1‑139 (MQ=255)
aTTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGcc < 2:563906/139‑1 (MQ=255)
gAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCg < 1:150522/138‑1 (MQ=255)
aagaagAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAgtggtg > 1:647833/1‑101 (MQ=255)
aagaagAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAgtggtg < 2:647833/101‑1 (MQ=255)
gTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGa > 1:762665/1‑84 (MQ=255)
gTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGa < 2:762665/84‑1 (MQ=255)
gTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGa > 1:198814/1‑138 (MQ=255)
cGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGatat < 2:407829/138‑1 (MQ=255)
|
GGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATAT > NZ_CP009273/437985‑438242
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ 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
GCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATCGATGAAC > NZ_CP009273/437999‑438259
|
GCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGT < SRR3722133.598187/151‑1 (MQ=60)
GCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAA > SRR3722133.736848/1‑150 (MQ=60)
ATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGC > SRR3722133.571393/1‑151 (MQ=60)
ATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGC > SRR3722133.723330/1‑151 (MQ=60)
GAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCG > SRR3722133.263351/1‑151 (MQ=60)
ATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGC > SRR3722133.548682/1‑150 (MQ=60)
GATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGT < SRR3722133.128114/150‑1 (MQ=60)
CCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAG < SRR3722133.494586/150‑1 (MQ=60)
CGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAA < SRR3722133.538009/151‑1 (MQ=60)
GGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAAT > SRR3722133.74395/1‑151 (MQ=60)
CAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGAGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGG > SRR3722133.415670/1‑151 (MQ=60)
GATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCtgtctcttatacacatctccgagccc > SRR3722133.656293/1‑124 (MQ=60)
TGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGAT < SRR3722133.152494/150‑1 (MQ=60)
GAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGctgtctcttatacacatctccgagcccacgagaccgtact > SRR3722133.772529/1‑106 (MQ=60)
GAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGAT > SRR3722133.201463/1‑150 (MQ=60)
TCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATCGATGAAC > SRR3722133.38543/1‑150 (MQ=60)
|
GCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATCGATGAAC > NZ_CP009273/437999‑438259
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
