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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
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%
| 87.9
/ NA
| 23 | Q521Q (CAG→CAA) | yciQ | DUF2207 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (10/13); total (10/13) |
GCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGT > NZ_CP009273/1320479‑1320637
|
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 2:447776/1‑90 (MQ=255)
gCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGAcaacaa > 1:887544/1‑90 (MQ=255)
ttACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTGCCCAAACTGGACAACAACGTTATGccc < 1:525464/90‑1 (MQ=255)
ttACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGccc < 2:700252/90‑1 (MQ=255)
aCCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCAc < 1:789952/90‑1 (MQ=255)
gTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACt < 1:27661/90‑1 (MQ=255)
tGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAag < 2:887544/90‑1 (MQ=255)
gTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgc < 2:538466/90‑1 (MQ=255)
atatTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGc > 2:843633/1‑58 (MQ=255)
atatTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGc < 1:843633/58‑1 (MQ=255)
atatTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTa > 2:819281/1‑60 (MQ=255)
atatTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTa < 1:819281/60‑1 (MQ=255)
atatTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgcag > 1:353367/1‑90 (MQ=255)
ttttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAac < 1:447776/90‑1 (MQ=255)
ttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacac > 2:652008/1‑90 (MQ=255)
ttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacac > 1:146134/1‑90 (MQ=255)
ttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacac > 2:81566/1‑90 (MQ=255)
ttCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAacac > 1:58963/1‑90 (MQ=255)
tCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGa > 1:514221/1‑48 (MQ=255)
tCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGa < 2:514221/48‑1 (MQ=255)
cTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAag < 2:425592/76‑1 (MQ=255)
cTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAag > 1:425592/1‑76 (MQ=255)
tttACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGt < 2:353367/90‑1 (MQ=255)
aCCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgc > 2:767829/1‑68 (MQ=255)
aCCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGgc < 1:767829/68‑1 (MQ=255)
|
GCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGT > NZ_CP009273/1320479‑1320637
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAAC > NZ_CP009273/1320469‑1320654
|
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAA > SRR3722072.902806/1‑100 (MQ=60)
CAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGC < SRR3722072.102598/100‑1 (MQ=60)
TTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTGCCCAAACTGGACAACAACGTTATGCCCACGGTGAAGC < SRR3722072.534916/100‑1 (MQ=60)
ACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTA < SRR3722072.803782/100‑1 (MQ=60)
cggagatgtgtataagagacagGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAAC < SRR3722072.858236/78‑1 (MQ=60)
gagatgtgtataagagacagGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTA < SRR3722072.833550/80‑1 (MQ=60)
GTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCG < SRR3722072.28148/100‑1 (MQ=60)
GGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAG > SRR3722072.359614/1‑100 (MQ=60)
GGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACAC > SRR3722072.148737/1‑100 (MQ=60)
GGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACAC > SRR3722072.60039/1‑100 (MQ=60)
GGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTctgtctcttatacacatctccgagcccacgag > SRR3722072.523476/1‑68 (MQ=60)
tataagagacagGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACAC < SRR3722072.781338/88‑1 (MQ=60)
GTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACctgt > SRR3722072.433326/1‑96 (MQ=60)
TTTTCTGCCAAAGTTTACCCAAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGA < SRR3722072.455974/100‑1 (MQ=60)
AAACTGGACAACAACGTTATGCCCACGGTGAAGCTctgtctcttatacacatctccgagcccacgagacgtccgattatctcgtatgccgtcttctgctt > SRR3722072.398741/1‑35 (MQ=59)
AAACTGGACAACAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAAC > SRR3722072.256798/1‑100 (MQ=60)
|
GTATATGCCAGCGGGTTATTTTACCGCTGTTTGCCTGACCGGTTATCTCACTGGCATGGGGTATATTTTTCTGCCAAAGTTTACCCAAACTGGACAGCAACGTTATGCCCACGGTGAAGCTATCGTTAACTATCTTGCGCGTAAAGAGGCAGCAACACACAGTGGACGTCGGCGGAAAGGGGAAAC > NZ_CP009273/1320469‑1320654
|
| 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: ‑ |
