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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,869,539 |
G→C |
P99A (CCG→GCG) |
nimR ← |
DNA‑binding transcriptional regulator NimR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,869,539 | 0 | G | C | 100.0%
| 57.4
/ NA
| 18 | P99A (CCG→GCG) | nimR | DNA‑binding transcriptional regulator NimR |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (10/8); total (10/8) |
CTGAGTCGTCGTCCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGGCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGT > NZ_CP009273/1869459‑1869624
|
cTGAGTCGTCGTCCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCAc > 1:255267/1‑90 (MQ=255)
tcCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGtt < 1:389233/90‑1 (MQ=255)
gTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGAt > 1:71167/1‑90 (MQ=255)
gggTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATaaacagaa > 1:356376/1‑90 (MQ=255)
taattCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTc < 1:63017/90‑1 (MQ=255)
aattCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCa > 1:1468/1‑90 (MQ=255)
ccGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCAtt < 2:356376/90‑1 (MQ=255)
ccGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCAtt < 1:454511/90‑1 (MQ=255)
cGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTa > 1:257839/1‑90 (MQ=255)
ggCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAg > 2:222072/1‑90 (MQ=255)
gATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCAtt > 1:307195/1‑77 (MQ=255)
gATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCAtt < 2:307195/77‑1 (MQ=255)
atatTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAACCAGAAAACAGACTTCAGCATTAGCTGTTACTTGAt < 2:257062/90‑1 (MQ=255)
ttttCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGc < 1:64266/90‑1 (MQ=255)
ttCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTa < 1:457638/90‑1 (MQ=255)
gCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCAc > 2:256752/1‑90 (MQ=255)
ttgtCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACcccgcccg > 2:257773/1‑90 (MQ=255)
gtCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGt > 1:219215/1‑90 (MQ=255)
|
CTGAGTCGTCGTCCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGGCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGT > NZ_CP009273/1869459‑1869624
|
| 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
GCTCAGCACGCTGAGTCGTCGTCCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGGCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGT > NZ_CP009273/1869449‑1869624
|
GCTCAGCACGCTGAGTCGTCGTCCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCAC < SRR3722087.161859/100‑1 (MQ=60)
GCTCAGCACGCTGAGTCGTCGTCCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCAC > SRR3722087.257741/1‑100 (MQ=60)
TCGTCGTCCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGAT > SRR3722087.71817/1‑100 (MQ=60)
TCCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAG < SRR3722087.393730/100‑1 (MQ=60)
CTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAA > SRR3722087.360383/1‑100 (MQ=60)
GGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCA > SRR3722087.1483/1‑100 (MQ=60)
AATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTA > SRR3722087.260342/1‑100 (MQ=60)
TAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCT < SRR3722087.63565/100‑1 (MQ=60)
CCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACT < SRR3722087.459806/100‑1 (MQ=60)
GCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTctg > SRR3722087.310408/1‑97 (MQ=60)
TTTTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCAC < SRR3722087.64829/100‑1 (MQ=60)
TTCAATGTGCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCC < SRR3722087.462966/100‑1 (MQ=60)
GCAACATGTTGTCGCCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGT > SRR3722087.221159/1‑100 (MQ=60)
|
GCTCAGCACGCTGAGTCGTCGTCCTGTTTGCCAGGGTTAAAATTAATTCCCGGCATAAGGGCGATATTTTCAATGTGCAACATGTTGTCGGCATTGTCACTGCGCTGGGTTCGATAAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGT > NZ_CP009273/1869449‑1869624
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
