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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
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%
| 85.8
/ NA
| 27 | D109A (GAC→GCC) | yegX | glycoside hydrolase family 25 protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (18/9); total (18/9) |
GGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGC > NZ_CP009273/2176720‑2176878
|
ggATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccac > 1:1405502/1‑90 (MQ=255)
ggATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccac > 1:487049/1‑90 (MQ=255)
gATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccacc > 1:722973/1‑90 (MQ=255)
gACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCttt > 2:1515553/1‑90 (MQ=255)
ggAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGcc < 1:88913/90‑1 (MQ=255)
ataatGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGt < 2:487049/90‑1 (MQ=255)
ataatGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGt < 2:309804/90‑1 (MQ=255)
atGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCtttt < 2:1012721/77‑1 (MQ=255)
atGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCtttt > 1:1012721/1‑77 (MQ=255)
gATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCt < 2:21887/90‑1 (MQ=255)
gATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGC‑TTTCGCCCTCCGTCGCCtt > 1:381185/1‑90 (MQ=255)
cGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaat > 1:1248378/1‑90 (MQ=255)
gCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaata > 1:87705/1‑90 (MQ=255)
ccACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATaaaa > 2:1418344/1‑90 (MQ=255)
cACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAg > 1:144747/1‑90 (MQ=255)
gcagcaGGCCATTTTCGCGGCTTAGTTTCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCaa < 1:785870/90‑1 (MQ=255)
gcagcaGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCaa < 2:624324/90‑1 (MQ=255)
gcagcaGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCaa < 2:722973/90‑1 (MQ=255)
cagGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTg > 2:881012/1‑90 (MQ=255)
ggCCATGTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTa > 2:1201115/1‑90 (MQ=255)
ttttCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCgg < 2:588906/90‑1 (MQ=255)
gcgGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATAcc > 2:294679/1‑90 (MQ=255)
tAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTc > 1:343279/1‑90 (MQ=255)
aCGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGc > 2:1159348/1‑90 (MQ=255)
aCGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGc > 2:626650/1‑90 (MQ=255)
aCGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGc > 2:1205813/1‑90 (MQ=255)
aCGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGc > 1:1168483/1‑90 (MQ=255)
|
GGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGC > NZ_CP009273/2176720‑2176878
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ 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
GCCTGAACTGAAGCGGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATC > NZ_CP009273/2176706‑2176897
|
tcgtcggcagcgtcagatgtgtataagagacagTAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGG < SRR3722078.1031052/67‑1 (MQ=60)
GAACTGAAGCGGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCAC > SRR3722078.1428289/1‑100 (MQ=60)
GAACTGAAGCGGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCAC > SRR3722078.492834/1‑100 (MQ=60)
AACTGAAGCGGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACC > SRR3722078.731949/1‑100 (MQ=60)
GGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCtg > SRR3722078.1027632/1‑98 (MQ=60)
GGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCC < SRR3722078.89962/100‑1 (MQ=60)
GAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGC‑TTTCGCCCTCCGTCGCCTT > SRR3722078.385838/1‑100 (MQ=60)
AATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAAT > SRR3722078.1268136/1‑100 (MQ=60)
ATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATA > SRR3722078.88740/1‑100 (MQ=60)
TGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAG > SRR3722078.146427/1‑100 (MQ=60)
GCAGCAGGCCATTTTCGCGGCTTAGTTTCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCG < SRR3722078.796114/100‑1 (MQ=60)
TTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTC > SRR3722078.347477/1‑100 (MQ=60)
GTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGC > SRR3722078.1186637/1‑100 (MQ=60)
ATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACTATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATC > SRR3722078.1414170/1‑100 (MQ=60)
|
GCCTGAACTGAAGCGGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATC > NZ_CP009273/2176706‑2176897
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
