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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
354,025 |
T→C |
E126G (GAA→GGA) |
cynR ← |
transcriptional regulator CynR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 354,025 | 0 | T | C | 100.0%
| 20.7
/ NA
| 8 | E126G (GAA→GGA) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (3/5); total (3/5) |
ACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTG > NZ_CP009273/353953‑354111
|
acaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg < 1:152470/90‑1 (MQ=255)
aTCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAgcgc > 2:169169/1‑90 (MQ=255)
caccTCGTCGCGGCAAAGAATATCCTCGATTTCCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATc < 1:374908/87‑1 (MQ=255)
gCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAggg > 1:116391/1‑90 (MQ=255)
aaGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGcc < 2:142480/90‑1 (MQ=255)
aaGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGcc < 2:252756/90‑1 (MQ=255)
tctcCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGGAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTaa > 1:328590/1‑90 (MQ=255)
aTTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTg < 1:197908/90‑1 (MQ=255)
|
ACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTG > NZ_CP009273/353953‑354111
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 25 ≤ 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
CCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATAC > NZ_CP009273/353933‑354121
|
CCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAG < SRR3722091.247983/100‑1 (MQ=60)
ACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGAT < SRR3722091.154710/100‑1 (MQ=60)
CACCTCGTCGCGGCAAAGAATATCCTCGATTTCCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAG < SRR3722091.381539/100‑1 (MQ=60)
ACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGG > SRR3722091.118153/1‑100 (MQ=60)
TCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGGAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAA > SRR3722091.334285/1‑100 (MQ=60)
ATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATAC < SRR3722091.200888/100‑1 (MQ=60)
|
CCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATAC > NZ_CP009273/353933‑354121
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
