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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
661,892 |
A→C |
G594G (GGT→GGG) |
mrdA ← |
peptidoglycan DD‑transpeptidase MrdA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 661,892 | 0 | A | C | 100.0%
| 65.2
/ NA
| 20 | G594G (GGT→GGG) | mrdA | peptidoglycan DD‑transpeptidase MrdA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (12/8); total (12/8) |
GGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACGC > NZ_CP009273/661812‑661976
|
ggcagATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTcc < 2:235421/90‑1 (MQ=255)
tATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAg > 2:213279/1‑90 (MQ=255)
tCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGcc < 1:141102/90‑1 (MQ=255)
cACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCa > 1:395269/1‑90 (MQ=255)
cccAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACt > 1:36059/1‑90 (MQ=255)
cATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCgg < 2:181401/90‑1 (MQ=255)
tAATGTGGTCGAGGATCTGGCCCATCAGTGTACAAACCGCCGGACCCGCCCCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt < 1:278175/90‑1 (MQ=255)
gtggAGGATCTGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt < 1:368124/80‑1 (MQ=255)
gTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt > 2:368124/1‑83 (MQ=255)
gTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTa > 2:3752/1‑90 (MQ=255)
gTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTa > 1:432565/1‑90 (MQ=255)
tCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTAt < 2:432565/90‑1 (MQ=255)
tCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTAt < 2:395269/90‑1 (MQ=255)
aaCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTtgtg > 1:196428/1‑90 (MQ=255)
aaCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTtgtg > 1:179632/1‑90 (MQ=255)
cgccgGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCgg > 2:358913/1‑51 (MQ=255)
cgccgGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCgg < 1:358913/51‑1 (MQ=255)
cgccgGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTc > 1:381352/1‑90 (MQ=255)
cgccgGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTc > 1:21859/1‑90 (MQ=255)
gCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACGc > 2:170173/1‑90 (MQ=255)
|
GGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACGC > NZ_CP009273/661812‑661976
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACCGCTGGATTTTCCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACGCTCGGCAA > NZ_CP009273/661794‑661983
|
ACCGCTGGATTTTCCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCC < SRR3722087.63880/100‑1 (MQ=60)
GTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCA > SRR3722087.399834/1‑100 (MQ=60)
GTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACT > SRR3722087.36349/1‑100 (MQ=60)
TCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAT < SRR3722087.142412/100‑1 (MQ=60)
GCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTA > SRR3722087.437623/1‑100 (MQ=60)
gtgggctcggagatgtgtataagagacagGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTAT < SRR3722087.362972/71‑1 (MQ=60)
TAATGTGGTGGAGGATCTGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGG < SRR3722087.372314/100‑1 (MQ=60)
TAATGTGGTCGAGGATCTGGCCCATCAGTGTACAAACCGCCGGACCCGCCCCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGG < SRR3722087.280931/100‑1 (MQ=60)
TCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTG > SRR3722087.181234/1‑100 (MQ=60)
TCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTG > SRR3722087.198159/1‑100 (MQ=60)
GTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > SRR3722087.22025/1‑100 (MQ=60)
GTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > SRR3722087.385741/1‑100 (MQ=60)
CCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACGCTCGGCAA > SRR3722087.211200/1‑100 (MQ=60)
|
ACCGCTGGATTTTCCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACGCTCGGCAA > NZ_CP009273/661794‑661983
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
