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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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%
| 60.6
/ NA
| 20 | D109A (GAC→GCC) | yegX | glycoside hydrolase family 25 protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (13/7); total (13/7) |
GATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCC > NZ_CP009273/2176721‑2176879
|
gATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccacc > 2:12996/1‑90 (MQ=255)
aTACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccacca < 2:92320/90‑1 (MQ=255)
gACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCttt > 2:305226/1‑90 (MQ=255)
gggAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGc > 2:234386/1‑90 (MQ=255)
taatGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTc < 2:255781/90‑1 (MQ=255)
gATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCt < 1:9863/90‑1 (MQ=255)
tACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAAGAGGGGGCCGCCAGCGTTTCGCCTTCCGTCGCCTta > 1:275238/1‑90 (MQ=255)
gCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaata > 2:13461/1‑90 (MQ=255)
gCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaata > 2:242028/1‑90 (MQ=255)
ccccACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaataa > 1:351388/1‑90 (MQ=255)
ccccACGCAGCAGGCCA‑TTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATaaa > 2:422270/1‑90 (MQ=255)
cagGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTg > 2:407595/1‑90 (MQ=255)
ggCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTa > 2:78484/1‑90 (MQ=255)
ccATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAg < 1:294125/90‑1 (MQ=255)
ccATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAg < 2:442272/90‑1 (MQ=255)
ttttCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCTAACTGTAAGCgg > 1:245111/1‑90 (MQ=255)
ttCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGAt < 1:251605/90‑1 (MQ=255)
gcgGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATAcc > 1:475787/1‑90 (MQ=255)
cAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCAtt > 2:4203/1‑90 (MQ=255)
cgcgAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGcc < 2:109878/90‑1 (MQ=255)
|
GATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCC > NZ_CP009273/2176721‑2176879
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 29 ≤ 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
GAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCG > NZ_CP009273/2176735‑2176867
|
GAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAAGAGGGGGCCGCCAGCGTTTCGCCTTCCGTCGCCTTA > SRR3722111.278649/1‑100 (MQ=60)
TAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAA > SRR3722111.356169/1‑100 (MQ=60)
GATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGC < SRR3722111.9988/100‑1 (MQ=60)
CAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCTAACTGTAAGCGG > SRR3722111.248011/1‑100 (MQ=60)
GGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACC > SRR3722111.483069/1‑100 (MQ=60)
CCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCAT < SRR3722111.297893/100‑1 (MQ=60)
TTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCG < SRR3722111.254562/100‑1 (MQ=60)
|
GAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCG > NZ_CP009273/2176735‑2176867
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
