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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 96.0%
| 75.0
/ ‑4.0
| 25 | D109A (GAC→GCC) | yegX | glycoside hydrolase family 25 protein |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base G (19/5); total (20/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
GATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCC > NZ_CP009273/2176721‑2176889
|
gATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGccacc > 1:591406/1‑90 (MQ=255)
ccGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCt > 1:749063/1‑90 (MQ=255)
gggAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGc > 1:514073/1‑90 (MQ=255)
aataatGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCtttt > 2:687416/1‑81 (MQ=255)
aataatGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCtttt < 1:687416/81‑1 (MQ=255)
ataatGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGt < 2:836684/90‑1 (MQ=255)
aCGCCCCACGCAGCAGGCCATTTTTGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaa > 1:429200/1‑90 (MQ=255)
aCGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaa > 1:412381/1‑90 (MQ=255)
cGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaat > 2:677632/1‑90 (MQ=255)
ccccACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaataa < 2:534198/90‑1 (MQ=255)
ccccACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTtaataa > 1:534198/1‑90 (MQ=255)
ccACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATaaaa > 2:789188/1‑90 (MQ=255)
aCGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGc > 2:506517/1‑90 (MQ=255)
gcagcaGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCaa < 1:783283/90‑1 (MQ=255)
gcagGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACt > 1:71416/1‑90 (MQ=255)
gcagGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACt > 1:76653/1‑90 (MQ=255)
gcagGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACt > 2:338600/1‑90 (MQ=255)
gcagGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACt > 1:486646/1‑90 (MQ=255)
gcagGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACt > 1:328249/1‑90 (MQ=255)
ttttCGCGGCTTAGTTGCCAGTTACGCGAGAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCgg > 1:142991/1‑90 (MQ=255)
gcgGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATAcc > 2:772145/1‑90 (MQ=255)
ggCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCAt < 2:450351/90‑1 (MQ=255)
cAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCAtt > 1:135387/1‑90 (MQ=255)
cAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCAtt > 1:292042/1‑90 (MQ=255)
aGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGcc > 1:418084/1‑90 (MQ=255)
|
GATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCC > NZ_CP009273/2176721‑2176889
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AACTGAAGCGGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATCCGCT > NZ_CP009273/2176711‑2176901
|
AACTGAAGCGGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACC > SRR3722079.597311/1‑100 (MQ=60)
GAAGCGGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCT > SRR3722079.757068/1‑100 (MQ=60)
tctctggtctcgtgggctcggagatgtgtataagagacaGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTT < SRR3722079.553296/61‑1 (MQ=60)
GATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGC > SRR3722079.518772/1‑100 (MQ=60)
ACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGT < SRR3722079.694640/100‑1 (MQ=60)
AAATAATGATACGCCCCACGCAGCAGGCCATTTTTGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAA > SRR3722079.432916/1‑100 (MQ=60)
AAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAA > SRR3722079.415910/1‑100 (MQ=60)
TAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAA > SRR3722079.539204/1‑100 (MQ=60)
GCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACT > SRR3722079.72011/1‑100 (MQ=60)
GCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACT > SRR3722079.77278/1‑100 (MQ=60)
GCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACT > SRR3722079.330875/1‑100 (MQ=60)
GCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACT > SRR3722079.490907/1‑100 (MQ=60)
GCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCG < SRR3722079.791678/100‑1 (MQ=60)
CAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAGAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGG > SRR3722079.144214/1‑100 (MQ=60)
GCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATT > SRR3722079.294446/1‑100 (MQ=60)
GCTTAGTTGCCAGTTACGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATT > SRR3722079.136530/1‑100 (MQ=60)
CGCGAAAAATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCC > SRR3722079.421688/1‑100 (MQ=60)
ATAGGGGGCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATC > SRR3722079.386047/1‑100 (MQ=60)
GGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATCCGCT > SRR3722079.226508/1‑100 (MQ=60)
|
AACTGAAGCGGATACCGACGGGGAGAAATAATGATACGCCCCACGCAGCAGGCCATTTTCGCGGCTTAGTTGCCAGTTACGCGAAAAATAGGGGTCCACCAGCTTTTCGCCTTCCGTCGCCTTAATAAAAGCAAACTGTAAGCGGATACCATTGTCGCGCATTTTTGCCACCCGCTGCCAGTCGATCCGCT > NZ_CP009273/2176711‑2176901
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
