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 |
4,350,381 |
G→C |
G457G (GGC→GGG) |
cadC ← |
lysine decarboxylation/transport transcriptional activator CadC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,350,381 | 0 | G | C | 100.0%
| 65.7
/ NA
| 20 | G457G (GGC→GGG) | cadC | lysine decarboxylation/transport transcriptional activator CadC |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (12/8); total (12/8) |
GGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350296‑4350465
|
gggTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCaa > 1:266089/1‑90 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa > 2:174843/1‑90 (MQ=255)
cTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAt > 1:117640/1‑90 (MQ=255)
atGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGc < 2:297105/90‑1 (MQ=255)
gCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCa > 1:213590/1‑90 (MQ=255)
cATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAg > 1:322437/1‑90 (MQ=255)
tCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTa > 2:176606/1‑90 (MQ=255)
cAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAgg < 1:417905/66‑1 (MQ=255)
cAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGACAgg > 2:417905/1‑66 (MQ=255)
aGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTAtt > 1:251021/1‑90 (MQ=255)
aGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTAtt > 2:411056/1‑90 (MQ=255)
tCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGcc < 1:276990/90‑1 (MQ=255)
ggTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGt > 2:460285/1‑90 (MQ=255)
gTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTa > 1:414102/1‑90 (MQ=255)
cTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATc < 2:466228/90‑1 (MQ=255)
cTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATc < 1:188717/90‑1 (MQ=255)
ttcatAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGtttt < 1:460285/90‑1 (MQ=255)
atAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacc > 1:476381/1‑90 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 1:365521/90‑1 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 2:476381/90‑1 (MQ=255)
|
GGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350296‑4350465
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCACTGA > NZ_CP009273/4350286‑4350478
|
ATCCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAA > SRR3722087.268706/1‑100 (MQ=60)
GTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAT > SRR3722087.118764/1‑100 (MQ=60)
tgtataagagacaGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAG < SRR3722087.422773/87‑1 (MQ=60)
GGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCA > SRR3722087.215461/1‑100 (MQ=60)
GTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAG > SRR3722087.325924/1‑100 (MQ=60)
GATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATT > SRR3722087.253454/1‑100 (MQ=60)
CTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTA > SRR3722087.418928/1‑100 (MQ=60)
TCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACT < SRR3722087.279733/100‑1 (MQ=60)
CCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACC > SRR3722087.481925/1‑100 (MQ=60)
gagacagTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCT < SRR3722087.453781/93‑1 (MQ=60)
CTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCT < SRR3722087.190377/100‑1 (MQ=60)
TTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACC < SRR3722087.465642/100‑1 (MQ=60)
ACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC < SRR3722087.369671/100‑1 (MQ=60)
TTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCACTGA > SRR3722087.1628/1‑100 (MQ=60)
|
ATCCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCACTGA > NZ_CP009273/4350286‑4350478
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
