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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,927,010 |
T→C |
K2E (AAA→GAA) |
kdgA ← |
bifunctional 4‑hydroxy‑2‑oxoglutarate aldolase/2‑dehydro‑3‑deoxy‑phosphogluconate aldolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,927,010 | 0 | T | C | 100.0%
| 41.8
/ NA
| 13 | K2E (AAA→GAA) | kdgA | bifunctional 4‑hydroxy‑2‑oxoglutarate aldolase/2‑dehydro‑3‑deoxy‑phosphogluconate aldolase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (4/9); total (4/9) |
CGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTTCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCACCGGAC > NZ_CP009273/1926927‑1927089
|
cgcgTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCag < 1:35545/90‑1 (MQ=255)
cGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTaaaa > 1:307028/1‑90 (MQ=255)
ggtCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACa < 2:41379/90‑1 (MQ=255)
ggATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTg < 2:340745/90‑1 (MQ=255)
ttgattCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTgtcg < 1:107870/65‑1 (MQ=255)
ttgattCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTgtcg > 2:107870/1‑65 (MQ=255)
ttgattCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTgcgc < 1:326310/90‑1 (MQ=255)
gattCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGccc < 2:304101/90‑1 (MQ=255)
tGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGTTTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGccc < 2:191937/85‑1 (MQ=255)
tGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGccc > 1:191937/1‑85 (MQ=255)
tGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGccc > 1:76633/1‑85 (MQ=255)
tGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGccc < 2:76633/85‑1 (MQ=255)
ttCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGATCGGCACCGGAc < 1:182517/90‑1 (MQ=255)
|
CGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTTCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCACCGGAC > NZ_CP009273/1926927‑1927089
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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
GGCACCGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTTCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCACCGGACAGTTTTTCAC > NZ_CP009273/1926922‑1927099
|
GGCACCGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTT < SRR3722090.23492/100‑1 (MQ=60)
CGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCT < SRR3722090.35912/100‑1 (MQ=60)
CCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAA > SRR3722090.310944/1‑100 (MQ=60)
gtgtataagagacaGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAG < SRR3722090.109026/86‑1 (MQ=60)
GGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTC > SRR3722090.194031/1‑100 (MQ=60)
GGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTC > SRR3722090.77481/1‑100 (MQ=60)
TTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGC < SRR3722090.330547/100‑1 (MQ=60)
TTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGATCGGCACCGGACAGTTTTTCAC < SRR3722090.184469/100‑1 (MQ=60)
|
GGCACCGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTTCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCACCGGACAGTTTTTCAC > NZ_CP009273/1926922‑1927099
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
