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 I178 R1
|
167 |
28.0 |
1137820 |
95.3% |
1084342 |
115.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,589,054 |
T→G |
T69P (ACC→CCC) |
opgB ← |
phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,589,054 | 0 | T | G | 100.0%
| 97.0
/ NA
| 28 | T69P (ACC→CCC) | opgB | phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (16/12); total (16/12) |
TGCGGATGATGGCGACGACGGCGCAGGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGTCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGTTAACGTGGCTGCAAACCACC > NZ_CP009273/4588942‑4589182
|
tGCGGATGATGGCGACGACGGCGCAGGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGaa > 1:168361/1‑139 (MQ=255)
cGGATGATGGCGACGACGGCGCAGGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAAcc > 1:502849/1‑139 (MQ=255)
cgcACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGtt < 2:475820/88‑1 (MQ=255)
cgcACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGtt > 1:475820/1‑88 (MQ=255)
cgcACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCAt > 2:85581/1‑119 (MQ=255)
cgcACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCAt < 1:85581/119‑1 (MQ=255)
cGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCaaa < 1:119700/139‑1 (MQ=255)
cGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCaaa > 2:119700/1‑139 (MQ=255)
tGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAg < 2:361448/76‑1 (MQ=255)
tGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAg > 1:361448/1‑76 (MQ=255)
ccAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAAc < 1:260759/139‑1 (MQ=255)
aGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTa > 2:474042/1‑64 (MQ=255)
aGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTa < 1:474042/64‑1 (MQ=255)
tGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGt < 2:540905/102‑1 (MQ=255)
tGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGt > 1:540905/1‑102 (MQ=255)
tGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAg > 2:152859/1‑139 (MQ=255)
cGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTa < 2:456832/54‑1 (MQ=255)
cGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTa > 1:456832/1‑54 (MQ=255)
aTACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGccc > 1:518750/1‑137 (MQ=255)
ggCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCg > 1:214285/1‑139 (MQ=255)
gCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTgg < 1:523121/42‑1 (MQ=255)
gCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTgg > 2:523121/1‑42 (MQ=255)
gCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGcc > 2:421100/1‑129 (MQ=255)
gCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGcc < 1:421100/129‑1 (MQ=255)
gCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGt > 2:95729/1‑139 (MQ=255)
gCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGt > 1:100605/1‑139 (MQ=255)
cTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGTTAACGTGGCTGCa < 2:241142/138‑1 (MQ=255)
ccAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGTTAACGTGGCTGCAAaccacc < 2:100605/139‑1 (MQ=255)
|
TGCGGATGATGGCGACGACGGCGCAGGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGTCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGTTAACGTGGCTGCAAACCACC > NZ_CP009273/4588942‑4589182
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ 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
GCGCCAGCAGGCTGTAACCAAAATGGTGCGGATGATGGCGACGACGGCGCAGGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGTCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGTTAACGTGGCTGCAAACCACCAGGTGTTACG > NZ_CP009273/4588916‑4589192
|
GCGCCAGCAGGCTGTAACCAAAATGGTGCGGATGATGGCGACGACGGCGCAGGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGT < SRR3722132.243508/151‑1 (MQ=60)
cagctcagtcttttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAG < SRR3722132.532379/64‑1 (MQ=60)
aagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacaGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGA < SRR3722132.482515/87‑1 (MQ=60)
AACCAAAATGGTGCGGATGATGGCGACGACGGCGCAGGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAAC > SRR3722132.171526/1‑151 (MQ=60)
CCAAAATGGTGCGGATGATGGCGACGACGGCGCAGGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCG > SRR3722132.511770/1‑151 (MQ=60)
aagagacaGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAA < SRR3722132.87164/142‑1 (MQ=60)
ATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGctgtctcttatacacatctccgagcccacgagaccgtact > SRR3722132.484319/1‑110 (MQ=60)
CCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCtgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgc > SRR3722132.368089/1‑99 (MQ=60)
CCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATAT < SRR3722132.121896/151‑1 (MQ=60)
CCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACctgtctcttatacacatctccgagccc > SRR3722132.550437/1‑124 (MQ=60)
CCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCC < SRR3722132.265716/151‑1 (MQ=60)
CAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGActgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaaaa > SRR3722132.465044/1‑76 (MQ=60)
GCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCC > SRR3722132.527960/1‑149 (MQ=60)
TGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGT > SRR3722132.218289/1‑151 (MQ=60)
GCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGTT > SRR3722132.102460/1‑151 (MQ=60)
GCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGTT < SRR3722132.428705/151‑1 (MQ=60)
CGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCtgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaaaaaaacaacaactaaataagcccg > SRR3722132.90482/1‑55 (MQ=60)
CGCCAGCACCGGGCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGTTAACGTGGCTGCAAACCACCAGGTGTTACG > SRR3722132.290074/1‑151 (MQ=60)
|
GCGCCAGCAGGCTGTAACCAAAATGGTGCGGATGATGGCGACGACGGCGCAGGATCCAGCCCAGCGCACCGAACACCGCTGTCAGCCCCAGCACAATGCCGATACCCGGCAAAATGTATTTGCTGACGCCAGCACCGGTCAGGCTGTTGGTTAAGGTATAGAGAACCGCGTCGTTAATACCATCGCCAGTAAAATAGTCGCTGGCAAACAGGGTGATATTTAAAACGACAAATAGCCCCAGCACCGTTAACGTGGCTGCAAACCACCAGGTGTTACG > NZ_CP009273/4588916‑4589192
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
