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 |
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%
| 82.4
/ NA
| 26 | G594G (GGT→GGG) | mrdA | peptidoglycan DD‑transpeptidase MrdA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (17/9); total (17/9) |
GCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > NZ_CP009273/661809‑661966
|
gcaggcagATCGGTGTTGTTATCCCCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTtc < 1:346537/90‑1 (MQ=255)
ggcagATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTcc > 1:488204/1‑90 (MQ=255)
tgttgtTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATgg > 1:233382/1‑90 (MQ=255)
tATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAg > 2:253836/1‑90 (MQ=255)
aGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGc > 2:389583/1‑90 (MQ=255)
cctAATGTGGTCGAGCATCCGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCgg < 1:37078/88‑1 (MQ=255)
atcaaTGGGGTCGAGGATCGGGCGCATAAGTATTCCAACCGCCGGCCCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCgg < 2:107779/87‑1 (MQ=255)
tAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt > 2:610450/1‑90 (MQ=255)
tAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt > 1:37987/1‑90 (MQ=255)
gTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGGCCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTa > 2:377489/1‑90 (MQ=255)
gTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTa > 1:370565/1‑90 (MQ=255)
gTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTa > 2:562423/1‑90 (MQ=255)
gTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTa > 1:490850/1‑90 (MQ=255)
ggATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGgcg > 1:205017/1‑90 (MQ=255)
ggCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAgg < 1:6567/90‑1 (MQ=255)
cAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGtcat < 2:370565/90‑1 (MQ=255)
aGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGtcatc < 2:142379/90‑1 (MQ=255)
aGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGtcatc < 2:215020/90‑1 (MQ=255)
gtACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGt > 2:61474/1‑90 (MQ=255)
aaCCGCCGGACCCGCACTCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCgg < 2:168489/77‑1 (MQ=255)
aaCCGCCGGACCCGCACTCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCgg > 1:168489/1‑77 (MQ=255)
aaCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTtgtg > 1:438380/1‑90 (MQ=255)
cgccgGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTc < 2:122111/90‑1 (MQ=255)
cgccgGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTc > 1:71377/1‑90 (MQ=255)
cgccgGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTc > 1:433203/1‑90 (MQ=255)
cgccgGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTc > 1:229851/1‑90 (MQ=255)
|
GCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > NZ_CP009273/661809‑661966
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ 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
ATTTTCCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > NZ_CP009273/661802‑661966
|
ATTTTCCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCC > SRR3722088.494019/1‑100 (MQ=60)
GCAGGCAGATCGGTGTTGTTATCCCCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCA < SRR3722088.350185/100‑1 (MQ=60)
GGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGG > SRR3722088.235694/1‑100 (MQ=60)
TCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAT > SRR3722088.38384/1‑100 (MQ=60)
GCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTA > SRR3722088.374494/1‑100 (MQ=60)
GCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTA > SRR3722088.496707/1‑100 (MQ=60)
CCTAATGTGGTCGAGCATCCGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTAT < SRR3722088.37468/100‑1 (MQ=60)
ATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCG > SRR3722088.207072/1‑100 (MQ=60)
GGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAG < SRR3722088.6654/100‑1 (MQ=60)
TCAGTGTACCAACCGCCGGACCCGCACTCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTCTG > SRR3722088.170188/1‑100 (MQ=60)
TCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTG > SRR3722088.443419/1‑100 (MQ=60)
GTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > SRR3722088.232135/1‑100 (MQ=60)
GTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > SRR3722088.438149/1‑100 (MQ=60)
GTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > SRR3722088.72113/1‑100 (MQ=60)
|
ATTTTCCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > NZ_CP009273/661802‑661966
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
