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 |
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%
| 31.3
/ NA
| 10 | S35A (TCG→GCG) | wcaF | colanic acid biosynthesis acetyltransferase WcaF |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (1/9); total (1/9) |
GGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCA > NZ_CP009273/2122185‑2122308
|
ggacgAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCa < 2:59151/90‑1 (MQ=255)
cgAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAat < 2:343490/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 1:13040/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 2:141914/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 2:33243/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 2:53526/90‑1 (MQ=255)
aCGTTTTTTCCTATTCTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGcc < 1:17216/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGccc < 1:336387/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGccc < 2:98378/90‑1 (MQ=255)
cGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCa > 2:236275/1‑90 (MQ=255)
|
GGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCA > NZ_CP009273/2122185‑2122308
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTG > NZ_CP009273/2122192‑2122306
|
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAC < SRR3722090.13178/100‑1 (MQ=60)
ACGTTTTTTCCTATTCTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCC < SRR3722090.17406/100‑1 (MQ=60)
CTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTG < SRR3722090.340771/100‑1 (MQ=60)
|
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTG > NZ_CP009273/2122192‑2122306
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
