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 |
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%
| 40.9
/ 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 (5/8); total (5/8) |
CGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTTCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCACC > NZ_CP009273/1926927‑1927085
|
cgcgTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCag < 1:294970/90‑1 (MQ=255)
cgcgTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCag < 1:306797/90‑1 (MQ=255)
gcgTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCaga > 1:268580/1‑90 (MQ=255)
aCCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGAtt < 1:347274/90‑1 (MQ=255)
cGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTtctc > 1:431752/1‑60 (MQ=255)
cGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTtctc < 2:431752/60‑1 (MQ=255)
cGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTaaaa < 1:384113/90‑1 (MQ=255)
cGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTaaaa < 2:278720/90‑1 (MQ=255)
gCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGt > 2:50294/1‑90 (MQ=255)
ggtggtCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGAt > 1:242120/1‑90 (MQ=255)
gattCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGccc < 1:48099/90‑1 (MQ=255)
gattCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGccc < 2:459667/90‑1 (MQ=255)
tGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCAcc > 2:466207/1‑90 (MQ=255)
|
CGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTTCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCACC > NZ_CP009273/1926927‑1927085
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
CATCGGCACCGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTTCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCAC > NZ_CP009273/1926918‑1927084
|
CATCGGCACCGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGA > SRR3722087.271223/1‑100 (MQ=60)
CGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCT < SRR3722087.297979/100‑1 (MQ=60)
CGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCT < SRR3722087.310003/100‑1 (MQ=60)
ACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGT < SRR3722087.351163/100‑1 (MQ=60)
CCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTctgtctcttatacacatctc > SRR3722087.436799/1‑80 (MQ=60)
CAACCGAGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGAT > SRR3722087.244419/1‑100 (MQ=60)
CGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAG < SRR3722087.388538/100‑1 (MQ=60)
GATTCTGCACTTGTTTTCCAGTTTTCCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCAC < SRR3722087.48500/100‑1 (MQ=60)
|
CATCGGCACCGCGTGTTCCAGTTTTTTTACCACGATAACCGGTACAACCGGGCCGGTGGTCAGGATTGATTCTGCACTTGTTTTCCAGTTTTTCATCAGAGTTTTCTCTCGCCTGATTACAAATTTGTCGTCTTAAAAAGTGATACAGGTTGCGCCCTGTTCGGCAC > NZ_CP009273/1926918‑1927084
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
