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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,320,565 |
G→A |
Q521Q (CAG→CAA) |
yciQ → |
DUF2207 domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,320,565 | 0 | G | A | 100.0%
| 24.7
/ NA
| 8 | Q521Q (CAG→CAA) | yciQ | DUF2207 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (5/3); total (5/3) |
AGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCA > NZ_CP009273/1320478‑1320622
|
aGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGacaaca > 2:392062/1‑90 (MQ=255)
gTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGtt > 1:366058/1‑90 (MQ=255)
gTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGaa > 2:4316/1‑90 (MQ=255)
tGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCg < 2:153116/90‑1 (MQ=255)
gACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGt > 2:294109/1‑90 (MQ=255)
aCCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGtt < 1:542269/90‑1 (MQ=255)
ttATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTa > 2:197342/1‑90 (MQ=255)
ctcACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCtt < 1:4471/90‑1 (MQ=255)
atTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgcagca > 2:430993/1‑90 (MQ=255)
|
AGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCA > NZ_CP009273/1320478‑1320622
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAG > NZ_CP009273/1320473‑1320614
|
ATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTT > SRR3722111.371204/1‑100 (MQ=60)
CAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGC < SRR3722111.591237/100‑1 (MQ=60)
ACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTG < SRR3722111.550795/100‑1 (MQ=60)
CTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAG < SRR3722111.4528/100‑1 (MQ=60)
|
ATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAG > NZ_CP009273/1320473‑1320614
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
