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 |
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%
| 56.6
/ NA
| 17 | E126G (GAA→GGA) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/9); total (8/9) |
GGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTG > NZ_CP009273/353944‑354105
|
ggCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGc < 2:763626/90‑1 (MQ=255)
gAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTgg < 2:386145/90‑1 (MQ=255)
cacaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGt < 2:514266/90‑1 (MQ=255)
acaGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTg < 1:409201/90‑1 (MQ=255)
caGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGa > 1:626053/1‑90 (MQ=255)
aGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGAt < 2:545620/90‑1 (MQ=255)
gcgAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTg > 1:652202/1‑90 (MQ=255)
gcgAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTg > 1:207934/1‑90 (MQ=255)
aTCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAgcgc > 1:728429/1‑90 (MQ=255)
aCGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAg > 1:397211/1‑90 (MQ=255)
cAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATc < 2:700184/90‑1 (MQ=255)
tcgCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCAtt > 2:735602/1‑90 (MQ=255)
cAAAGCATATCCTCGATTTTCCCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAgggg < 1:215189/90‑1 (MQ=255)
aaGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGcc < 2:24113/90‑1 (MQ=255)
tatCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATaa > 2:543672/1‑90 (MQ=255)
tCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAg > 2:461824/1‑90 (MQ=255)
tGCGACATTCCCTGAAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTg < 2:452996/90‑1 (MQ=255)
|
GGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTG > NZ_CP009273/353944‑354105
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ 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
CTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGC > NZ_CP009273/353934‑354123
|
CTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGC < SRR3722073.357440/100‑1 (MQ=60)
CTCAAGCTCCGGCGAATGCACAGGCCCGAAGGCAATCCCAACGTCCATCTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGC < SRR3722073.619890/100‑1 (MQ=60)
GGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGA > SRR3722073.639044/1‑100 (MQ=60)
ATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTG > SRR3722073.212194/1‑100 (MQ=60)
ATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTG > SRR3722073.665605/1‑100 (MQ=60)
ACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGAT < SRR3722073.417944/100‑1 (MQ=60)
CGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGC > SRR3722073.743121/1‑100 (MQ=60)
GGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAG > SRR3722073.405668/1‑100 (MQ=60)
CAAAGCATATCCTCGATTTTCCCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGT < SRR3722073.219626/100‑1 (MQ=60)
GCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGGCGGC > SRR3722073.729752/1‑100 (MQ=60)
TCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGC > SRR3722073.603045/1‑100 (MQ=60)
|
CTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGC > NZ_CP009273/353934‑354123
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
