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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,122,267 |
A→C |
S35A (TCG→GCG) |
wcaF ← |
colanic acid biosynthesis acetyltransferase WcaF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,122,267 | 0 | A | C | 100.0%
| 31.8
/ NA
| 11 | S35A (TCG→GCG) | wcaF | colanic acid biosynthesis acetyltransferase WcaF |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (6/5); total (6/5) |
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAA > NZ_CP009273/2122180‑2122352
|
cTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGccc < 1:418671/90‑1 (MQ=255)
cTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGccc < 2:9775/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 1:215583/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 2:208897/90‑1 (MQ=255)
tACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGc > 1:399795/1‑90 (MQ=255)
gTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTg < 1:169171/90‑1 (MQ=255)
gTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTg > 2:268884/1‑90 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGccc < 1:173865/90‑1 (MQ=255)
ccGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc < 2:158213/90‑1 (MQ=255)
aataaAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCg > 2:68505/1‑90 (MQ=255)
aTACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGGCGCCCCGGAACCCTTTCGGCa > 1:129777/1‑90 (MQ=255)
ggCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGaaa > 1:356327/1‑90 (MQ=255)
ggCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGaaa > 2:231769/1‑90 (MQ=255)
|
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAA > NZ_CP009273/2122180‑2122352
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 29 ≤ 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
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCT > NZ_CP009273/2122180‑2122364
|
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAT < SRR3722094.425967/100‑1 (MQ=60)
GACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGC > SRR3722094.406697/1‑100 (MQ=60)
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAC < SRR3722094.218489/100‑1 (MQ=60)
GTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCAC < SRR3722094.171531/100‑1 (MQ=60)
CTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTG < SRR3722094.176278/100‑1 (MQ=60)
CAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGGCGCCCCGGAACCCTTTCGGCA > SRR3722094.131644/1‑100 (MQ=60)
CAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAA > SRR3722094.362288/1‑100 (MQ=60)
CGCCCCGGCAAATATTGTTGCCTGTACTGCCCCCCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCT < SRR3722094.269247/100‑1 (MQ=60)
|
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAATCT > NZ_CP009273/2122180‑2122364
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
