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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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%
| 41.8
/ NA
| 12 | Q521Q (CAG→CAA) | yciQ | DUF2207 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (4/8); total (4/8) |
GCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACAC > NZ_CP009273/1320479‑1320628
|
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 2:118419/1‑90 (MQ=255)
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 2:51265/1‑90 (MQ=255)
ttACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGccc < 1:472632/90‑1 (MQ=255)
aCCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCAc < 2:138361/90‑1 (MQ=255)
ccGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACg > 1:593253/1‑90 (MQ=255)
ccGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACg > 1:629479/1‑90 (MQ=255)
ttGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGc < 1:526595/90‑1 (MQ=255)
ttGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGc < 2:747974/90‑1 (MQ=255)
tcACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTg < 1:295839/90‑1 (MQ=255)
cACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTgc < 1:51265/90‑1 (MQ=255)
cTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTgcgc < 1:524366/90‑1 (MQ=255)
gggTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 1:766986/1‑42 (MQ=255)
gggTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa < 2:766986/42‑1 (MQ=255)
atatTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgcag > 1:584861/1‑90 (MQ=255)
ttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacac < 1:251275/90‑1 (MQ=255)
cTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacacac > 2:702510/1‑90 (MQ=255)
|
GCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACAC > NZ_CP009273/1320479‑1320628
|
| 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
GGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAACACGGA > NZ_CP009273/1320482‑1320659
|
GGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACG > SRR3722073.605642/1‑100 (MQ=60)
GGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACG > SRR3722073.642525/1‑100 (MQ=60)
TTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGC < SRR3722073.482693/100‑1 (MQ=60)
TTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAAC < SRR3722073.537637/100‑1 (MQ=60)
TCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGA < SRR3722073.302100/100‑1 (MQ=60)
CACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCctgtctcttatacacatctgacgctgccgacgatggcg > SRR3722073.782468/1‑62 (MQ=60)
CACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAG < SRR3722073.52471/100‑1 (MQ=60)
CTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGC < SRR3722073.535371/100‑1 (MQ=60)
GGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAG > SRR3722073.597075/1‑100 (MQ=60)
TTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACG < SRR3722073.256556/100‑1 (MQ=60)
GGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAACACGGA > SRR3722073.206834/1‑100 (MQ=60)
|
GGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAACACGGA > NZ_CP009273/1320482‑1320659
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
