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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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%
| 45.6
/ NA
| 15 | D109A (GAC→GCC) | yegX | glycoside hydrolase family 25 protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (6/9); total (6/9) |
GGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCC > NZ_CP009273/2176732‑2176879
|
ggAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGcc < 1:332917/90‑1 (MQ=255)
gATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCt < 1:412207/90‑1 (MQ=255)
tACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTta > 1:63359/1‑90 (MQ=255)
cGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaat < 2:82665/90‑1 (MQ=255)
aCGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGc < 2:152667/90‑1 (MQ=255)
aCGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGc < 2:495093/90‑1 (MQ=255)
gcagcaGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCaa < 2:20227/90‑1 (MQ=255)
gcagGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACt > 2:178742/1‑90 (MQ=255)
ggCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccacca > 1:454689/1‑51 (MQ=255)
ggCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccacca < 2:454689/51‑1 (MQ=255)
ggCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCaa > 1:251035/1‑84 (MQ=255)
ggCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCaa < 2:251035/84‑1 (MQ=255)
ggCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTa > 1:181829/1‑90 (MQ=255)
ttttCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCgg > 2:189682/1‑90 (MQ=255)
cgcgAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGcc < 2:250211/90‑1 (MQ=255)
|
GGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCC > NZ_CP009273/2176732‑2176879
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATCC > NZ_CP009273/2176732‑2176898
|
GGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCC < SRR3722092.338803/100‑1 (MQ=60)
GAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTA > SRR3722092.64391/1‑100 (MQ=60)
GATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGC < SRR3722092.420157/100‑1 (MQ=60)
CCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCctgtctcttatacacatctgacgctgccg > SRR3722092.463650/1‑71 (MQ=60)
CCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTA > SRR3722092.184856/1‑100 (MQ=60)
CCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTA > SRR3722092.255097/1‑100 (MQ=60)
TAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCctgtctcttatacacatctgacgctgccgacgaccatcttagtgtagatctcggtg > SRR3722092.393435/1‑44 (MQ=60)
|
GGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATCC > NZ_CP009273/2176732‑2176898
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
