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 F2 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,670,359 |
T→C |
G454G (GGA→GGG) |
yphE ← |
sugar ABC transporter ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,670,359 | 0 | T | C | 100.0%
| 45.7
/ NA
| 15 | G454G (GGA→GGG) | yphE | sugar ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/4); total (11/4) |
CGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > NZ_CP009273/2670283‑2670440
|
cgtgcTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagcca < 2:167793/90‑1 (MQ=255)
aataaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg < 2:481074/90‑1 (MQ=255)
aaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACa > 1:522983/1‑90 (MQ=255)
cAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAAt < 1:268314/90‑1 (MQ=255)
cAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAAt < 2:60057/90‑1 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACg > 2:300931/1‑90 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTACACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGACAGCTCAGGGACAATACg > 1:27718/1‑90 (MQ=255)
aGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTTTTTg > 2:38880/1‑90 (MQ=255)
aGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTg > 1:567887/1‑90 (MQ=255)
aaCTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCg > 1:654164/1‑90 (MQ=255)
gaTAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTgg > 1:281974/1‑90 (MQ=255)
tAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCt > 2:39585/1‑90 (MQ=255)
acGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGc > 1:279451/1‑90 (MQ=255)
acGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGc > 1:551763/1‑90 (MQ=255)
acGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGc > 2:387287/1‑90 (MQ=255)
|
CGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > NZ_CP009273/2670283‑2670440
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ 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
GTGAAACTCCTGCGAGAACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAA > NZ_CP009273/2670260‑2670445
|
GTGAAACTCCTGCGAGAACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTC < SRR3722088.381860/100‑1 (MQ=60)
GTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACA > SRR3722088.529306/1‑100 (MQ=60)
GTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTACACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGACAGCTCAGGGACAATACG > SRR3722088.28010/1‑100 (MQ=60)
CAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATC < SRR3722088.270909/100‑1 (MQ=60)
GTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTG > SRR3722088.574853/1‑100 (MQ=60)
CACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCG > SRR3722088.662271/1‑100 (MQ=60)
CTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGG > SRR3722088.284690/1‑100 (MQ=60)
GATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTctgtctcttatacacatctccgagcccacgagaccgtactagatctcgta > SRR3722088.616658/1‑50 (MQ=60)
GATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > SRR3722088.282140/1‑100 (MQ=60)
GATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > SRR3722088.558514/1‑100 (MQ=60)
ACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAA > SRR3722088.351087/1‑100 (MQ=60)
|
GTGAAACTCCTGCGAGAACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAA > NZ_CP009273/2670260‑2670445
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
