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 |
1,331,016 |
A→G |
Y310C (TAT→TGT) |
acnA → |
aconitate hydratase AcnA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,331,016 | 0 | A | G | 100.0%
| 22.2
/ NA
| 9 | Y310C (TAT→TGT) | acnA | aconitate hydratase AcnA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (4/5); total (4/5) |
GTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATATGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGC > NZ_CP009273/1330940‑1331083
|
gtcgAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCtgt < 1:66839/90‑1 (MQ=255)
gAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGc < 1:358293/80‑1 (MQ=255)
gAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGc > 2:358293/1‑80 (MQ=255)
aCTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGct > 1:258146/1‑65 (MQ=255)
aCTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGct < 2:258146/65‑1 (MQ=255)
gTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTa > 1:160229/1‑90 (MQ=255)
gTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTa > 2:183522/1‑90 (MQ=255)
ccaTTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGgc < 2:157970/90‑1 (MQ=255)
aTTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGgcgc < 2:387313/90‑1 (MQ=255)
|
GTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATATGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGC > NZ_CP009273/1330940‑1331083
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ 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
GAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATATGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTA > NZ_CP009273/1330933‑1331064
|
GAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGC < SRR3722113.361967/100‑1 (MQ=60)
GTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCC < SRR3722113.67425/100‑1 (MQ=60)
GTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCtgtctcttatacac > SRR3722113.260411/1‑86 (MQ=60)
ATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTA > SRR3722113.161545/1‑100 (MQ=60)
|
GAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATATGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTA > NZ_CP009273/1330933‑1331064
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
