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 |
4,215,724 |
T→G |
W657G (TGG→GGG) |
metH → |
methionine synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,215,724 | 0 | T | G | 82.9%
| 94.6
/ 10.5
| 35 | W657G (TGG→GGG) | metH | methionine synthase |
| Reads supporting (aligned to +/- strand): ref base T (2/4); new base G (11/18); total (13/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC > NZ_CP009273/4215640‑4215808
|
gAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGaa > 2:422606/1‑90 (MQ=255)
aGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAg < 1:191529/90‑1 (MQ=255)
aGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAg < 1:47680/90‑1 (MQ=255)
aGCGTTTACTGGAGCTTGCCGAGAAATAGCGGGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAg < 2:514486/90‑1 (MQ=255)
gCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGt > 1:119585/1‑90 (MQ=255)
gTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGa > 1:487584/1‑90 (MQ=255)
aCTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATaa < 2:382397/90‑1 (MQ=255)
ggAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACg < 2:408789/90‑1 (MQ=255)
gAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGt > 1:241338/1‑90 (MQ=255)
gCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCt > 1:299735/1‑90 (MQ=255)
gCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCt > 2:440913/1‑90 (MQ=255)
atatCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCt < 1:462131/90‑1 (MQ=255)
ggCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCaaa < 1:819413/90‑1 (MQ=255)
ggCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCaaa > 2:175338/1‑90 (MQ=255)
ggCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCaaa < 2:693942/90‑1 (MQ=255)
cagcaAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAgg < 2:612917/90‑1 (MQ=255)
aCCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTAcc < 1:77742/90‑1 (MQ=255)
aCCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTAcc < 1:411315/90‑1 (MQ=255)
cgacACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGtt > 2:457193/1‑90 (MQ=255)
cacCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTAt < 2:636735/90‑1 (MQ=255)
ccGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCg > 1:691337/1‑90 (MQ=255)
ccGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCt < 1:655271/64‑1 (MQ=255)
ccGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCt > 2:655271/1‑64 (MQ=255)
ccACCGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGGTGGTCAAAGGCATTACCGAGTTTATCGAGc < 2:776602/90‑1 (MQ=255)
ccAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc < 2:604838/90‑1 (MQ=255)
ccAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc < 1:475819/90‑1 (MQ=255)
ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc < 2:85569/90‑1 (MQ=255)
ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc < 1:740039/90‑1 (MQ=255)
ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc < 1:351403/90‑1 (MQ=255)
ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc < 1:323147/90‑1 (MQ=255)
cGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGa < 2:691337/90‑1 (MQ=255)
cagcagGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATAcc < 1:422606/90‑1 (MQ=255)
gCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCgaagaa > 1:486001/1‑90 (MQ=255)
tGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGc > 1:770989/1‑90 (MQ=255)
gcTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCcagc > 1:21886/1‑90 (MQ=255)
|
GAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC > NZ_CP009273/4215640‑4215808
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ 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
ATGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGCAGGCTACGCGCCCGA > NZ_CP009273/4215632‑4215823
|
ATGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGT > SRR3722079.120568/1‑100 (MQ=60)
TGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTG < SRR3722079.638812/100‑1 (MQ=60)
GGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGA > SRR3722079.491863/1‑100 (MQ=60)
AGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACG < SRR3722079.193190/100‑1 (MQ=60)
AGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACG < SRR3722079.48044/100‑1 (MQ=60)
GCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGT > SRR3722079.243369/1‑100 (MQ=60)
GTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCT > SRR3722079.302190/1‑100 (MQ=60)
tgtgtataagagacagACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGC < SRR3722079.662063/84‑1 (MQ=60)
ATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGC < SRR3722079.466175/100‑1 (MQ=60)
GGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCG < SRR3722079.828192/100‑1 (MQ=60)
ACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCG > SRR3722079.698607/1‑100 (MQ=60)
ACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCG < SRR3722079.414832/100‑1 (MQ=60)
ACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCG < SRR3722079.78376/100‑1 (MQ=60)
CCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA < SRR3722079.479975/100‑1 (MQ=60)
CCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA < SRR3722079.354167/100‑1 (MQ=60)
CCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA < SRR3722079.747953/100‑1 (MQ=60)
CCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGA < SRR3722079.325744/100‑1 (MQ=60)
CGCCAAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAA > SRR3722079.490249/1‑100 (MQ=60)
CAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCC < SRR3722079.426251/100‑1 (MQ=60)
GCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGC > SRR3722079.779244/1‑100 (MQ=60)
GCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC > SRR3722079.22036/1‑100 (MQ=60)
GGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGCAGGCTACGCGCCCGA > SRR3722079.653319/1‑100 (MQ=60)
|
ATGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGCAGGCTACGCGCCCGA > NZ_CP009273/4215632‑4215823
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
