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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
463,972 |
A→G |
D45G (GAC→GGC) |
decR → |
DNA‑binding transcriptional regulator DecR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 463,972 | 0 | A | G | 100.0%
| 37.5
/ NA
| 13 | D45G (GAC→GGC) | decR | DNA‑binding transcriptional regulator DecR |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (6/7); total (6/7) |
TTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGACGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAAC > NZ_CP009273/463886‑464058
|
ttGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGAcggcgg < 1:376663/90‑1 (MQ=255)
ttGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGAcggcgg < 2:359970/90‑1 (MQ=255)
gCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGGTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTa > 2:496213/1‑90 (MQ=255)
ctctctTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCtt > 2:443789/1‑90 (MQ=255)
ttGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGc < 1:463057/90‑1 (MQ=255)
gCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGAcggcgg < 1:187088/71‑1 (MQ=255)
gCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGAcggcgg > 2:187088/1‑71 (MQ=255)
aCTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGc < 1:547628/90‑1 (MQ=255)
cTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGcc < 1:363207/90‑1 (MQ=255)
gTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCg > 1:173992/1‑90 (MQ=255)
gTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCg > 1:139295/1‑90 (MQ=255)
accCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTc < 2:533849/90‑1 (MQ=255)
tGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTg < 2:187118/90‑1 (MQ=255)
tGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGAcc < 2:524414/90‑1 (MQ=255)
gAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGc > 1:481650/1‑90 (MQ=255)
gAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGc > 2:21932/1‑90 (MQ=255)
cTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATaaaa < 1:223719/90‑1 (MQ=255)
acggcgGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAAc < 1:391498/90‑1 (MQ=255)
|
TTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGACGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAAC > NZ_CP009273/463886‑464058
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
ACTGCAGCAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGACGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAGCGA > NZ_CP009273/463874‑464071
|
ACTGCAGCAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGC > SRR3722111.437197/1‑100 (MQ=60)
CAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCC < SRR3722111.559410/100‑1 (MQ=60)
aagagacagCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATC < SRR3722111.189421/91‑1 (MQ=60)
TTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATC < SRR3722111.382044/100‑1 (MQ=60)
TTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCC < SRR3722111.470109/100‑1 (MQ=60)
ACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGAT < SRR3722111.556238/100‑1 (MQ=60)
CTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATC < SRR3722111.368279/100‑1 (MQ=60)
GGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCG > SRR3722111.141044/1‑100 (MQ=60)
GGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCG > SRR3722111.176160/1‑100 (MQ=60)
CCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGC > SRR3722111.489028/1‑100 (MQ=60)
CTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATC < SRR3722111.226431/100‑1 (MQ=60)
GAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACA > SRR3722111.498638/1‑100 (MQ=60)
ACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAG < SRR3722111.397169/100‑1 (MQ=60)
GCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAGCGA > SRR3722111.194311/1‑100 (MQ=60)
|
ACTGCAGCAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGACGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAGCGA > NZ_CP009273/463874‑464071
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
