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 |
2,176,805 |
T→G |
D109A (GAC→GCC) |
yegX ← |
glycoside hydrolase family 25 protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,176,805 | 0 | T | G | 100.0%
| 51.7
/ NA
| 16 | D109A (GAC→GCC) | yegX | glycoside hydrolase family 25 protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (11/5); total (11/5) |
GGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTG > NZ_CP009273/2176720‑2176887
|
ggATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccac > 2:336174/1‑90 (MQ=255)
gATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccacc < 2:388302/90‑1 (MQ=255)
ggAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGcc < 2:465056/90‑1 (MQ=255)
gATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCt > 1:226537/1‑90 (MQ=255)
gATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCt > 2:37273/1‑90 (MQ=255)
tACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTta > 1:412965/1‑90 (MQ=255)
tACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTta > 2:205523/1‑90 (MQ=255)
ccACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATaaaa > 1:581775/1‑90 (MQ=255)
aCGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGc > 1:20936/1‑90 (MQ=255)
aCGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGc > 1:756976/1‑90 (MQ=255)
aCGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGc > 2:290621/1‑90 (MQ=255)
cagGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTg > 2:488813/1‑90 (MQ=255)
ccATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAg < 1:86318/90‑1 (MQ=255)
cgcgAAAAATAGGGGGCCACCAGCTTTTCGCCTTTCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGcc < 2:267287/90‑1 (MQ=255)
gAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCAcc > 1:374988/1‑90 (MQ=255)
aTAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTg < 1:386818/90‑1 (MQ=255)
|
GGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTG > NZ_CP009273/2176720‑2176887
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ 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
GAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATC > NZ_CP009273/2176733‑2176897
|
GAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCT > SRR3722073.231265/1‑100 (MQ=60)
GAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTA > SRR3722073.421788/1‑100 (MQ=60)
ATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAA > SRR3722073.593921/1‑100 (MQ=60)
GATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGC > SRR3722073.21470/1‑100 (MQ=60)
GATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGC > SRR3722073.772280/1‑100 (MQ=60)
CCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCAT < SRR3722073.88261/100‑1 (MQ=60)
CCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACC > SRR3722073.382953/1‑100 (MQ=60)
ATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATC < SRR3722073.395056/100‑1 (MQ=60)
|
GAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATC > NZ_CP009273/2176733‑2176897
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
