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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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%
| 35.3
/ NA
| 12 | E126G (GAA→GGA) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/7); total (5/7) |
ATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCC > NZ_CP009273/353949‑354083
|
aTGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCt < 1:503161/80‑1 (MQ=255)
aTGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCt > 2:503161/1‑80 (MQ=255)
caGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCt > 1:280279/1‑75 (MQ=255)
caGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCt < 2:280279/75‑1 (MQ=255)
aCGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAg > 2:320475/1‑90 (MQ=255)
cAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAgggg < 1:1563/90‑1 (MQ=255)
cAAAGCATATCCTCGATTTTCCCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAgggg < 1:338696/90‑1 (MQ=255)
aaGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGcc < 1:158339/90‑1 (MQ=255)
cGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGGAATCCGCCATTAAGGGGcc < 1:186371/79‑1 (MQ=255)
cGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGGAATCCGCCATTAAGGGGcc > 2:186371/1‑79 (MQ=255)
ttCTCCTGCGACATTCCCTGTAGCTGGAGCGTGAt > 1:451018/1‑35 (MQ=39)
ttCTCCTGCGACATTCCCTGTAGCTGGAGCGTGAt < 2:451018/35‑1 (MQ=39)
|
ATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCC > NZ_CP009273/353949‑354083
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGAATTGCCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGCA > NZ_CP009273/353926‑354124
|
GGAATTGCCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTC < SRR3722094.322815/100‑1 (MQ=60)
GCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAG < SRR3722094.512025/100‑1 (MQ=60)
GGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCtgtc > SRR3722094.284491/1‑96 (MQ=60)
CAAAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGT < SRR3722094.1584/100‑1 (MQ=60)
CAAAGCATATCCTCGATTTTCCCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGT < SRR3722094.344273/100‑1 (MQ=60)
GAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGGAATCCGCCATTAAGGGGCCGATAAAGTAG < SRR3722094.188924/100‑1 (MQ=60)
AAGCATATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAG < SRR3722094.160547/100‑1 (MQ=60)
ATCCTCGATTTTCTCCTGCGACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCtgtctcttatacacatctgacgctgccgacgaccatcttagtgt > SRR3722094.458949/1‑56 (MQ=60)
ACATTCCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGAT > SRR3722094.150252/1‑100 (MQ=60)
CCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGGGACGGCGATACGCA > SRR3722094.125736/1‑100 (MQ=60)
|
GGAATTGCCTCCAGCTCCGGCGAATGCACAGGCGCGAAGGCAATCCCAACGTCCAACTCGTCGCGGCAAAGCATATCCTCGATTTTCTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGCA > NZ_CP009273/353926‑354124
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
