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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,661,508 |
T→G |
T250P (ACC→CCC) |
hcaR ← |
DNA‑binding transcriptional regulator HcaR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,661,508 | 0 | T | G | 100.0%
| 23.1
/ NA
| 9 | T250P (ACC→CCC) | hcaR | DNA‑binding transcriptional regulator HcaR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (3/6); total (3/6) |
TTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATT > NZ_CP009273/2661441‑2661586
|
ttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCg < 1:10139/90‑1 (MQ=255)
gTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGa < 1:266857/90‑1 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGc > 2:165576/1‑90 (MQ=255)
ggAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGccc > 1:107119/1‑90 (MQ=255)
tttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc < 1:370339/90‑1 (MQ=255)
tttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc < 1:376084/90‑1 (MQ=255)
aacCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATAtt < 2:453586/90‑1 (MQ=255)
tGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGccc < 1:127983/48‑1 (MQ=255)
tGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGccc > 2:127983/1‑48 (MQ=255)
|
TTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATT > NZ_CP009273/2661441‑2661586
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
TTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGG > NZ_CP009273/2661441‑2661573
|
TTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAG < SRR3722113.10236/100‑1 (MQ=60)
GTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCC > SRR3722113.108069/1‑100 (MQ=60)
GTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCC < SRR3722113.269209/100‑1 (MQ=60)
ctcgtgggctcggagatgtgtataagagacaGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGC < SRR3722113.129063/69‑1 (MQ=60)
TTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGG < SRR3722113.374181/100‑1 (MQ=60)
TTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGG < SRR3722113.379987/100‑1 (MQ=60)
|
TTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGG > NZ_CP009273/2661441‑2661573
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
