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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,980,420 |
A→G |
G5G (GGA→GGG) |
ftnB → |
non‑heme ferritin‑like protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,980,420 | 0 | A | G | 96.0%
| 78.2
/ ‑3.4
| 25 | G5G (GGA→GGG) | ftnB | non‑heme ferritin‑like protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (13/11); minor base T (0/1); total (13/12) |
| Fisher's exact test for biased strand distribution p-value = 4.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.69e-01 |
CTGCAAACAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGAATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTG > NZ_CP009273/1980336‑1980502
|
cTGCAAACAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCt < 2:17517/90‑1 (MQ=255)
tAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAaactc < 1:366244/90‑1 (MQ=255)
aaTTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAaactca < 1:386788/90‑1 (MQ=255)
ggTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACtctc > 1:327372/1‑90 (MQ=255)
tATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGTATGCTTCTCAAACTCAACTCTCAAATGAACcgcg < 2:445190/90‑1 (MQ=255)
tctcCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCa > 1:206525/1‑90 (MQ=255)
tctcCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCa > 2:189273/1‑90 (MQ=255)
ccACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATcc < 2:327372/90‑1 (MQ=255)
cTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAAtctc < 2:337026/90‑1 (MQ=255)
cTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAAtctc < 2:220738/90‑1 (MQ=255)
ggATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTa < 1:389489/90‑1 (MQ=255)
taAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTc > 1:350880/1‑90 (MQ=255)
ggATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCAcc < 2:131009/90‑1 (MQ=255)
atatTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTg > 1:159062/1‑90 (MQ=255)
atatTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTg > 1:121559/1‑90 (MQ=255)
atTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAg > 2:166874/1‑90 (MQ=255)
atTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAg > 1:397699/1‑90 (MQ=255)
gTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACt > 2:317142/1‑90 (MQ=255)
tATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAAtctc > 1:58428/1‑70 (MQ=255)
tATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAAtctc < 2:58428/70‑1 (MQ=255)
aTGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCt < 1:440397/80‑1 (MQ=255)
aTGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCt > 2:440397/1‑80 (MQ=255)
aTGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTgg < 2:500058/90‑1 (MQ=255)
tGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGgt > 1:165157/1‑90 (MQ=255)
ccGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTg > 2:468299/1‑90 (MQ=255)
|
CTGCAAACAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGAATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTG > NZ_CP009273/1980336‑1980502
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
CAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGAATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTGAACAGAGTCT > NZ_CP009273/1980343‑1980512
|
CAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTC > SRR3722114.330990/1‑100 (MQ=60)
gacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAA < SRR3722114.146432/43‑1 (MQ=60)
TAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAA < SRR3722114.370586/100‑1 (MQ=60)
AATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAAT < SRR3722114.391469/100‑1 (MQ=60)
ATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCA > SRR3722114.208529/1‑100 (MQ=60)
CTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTC > SRR3722114.354917/1‑100 (MQ=60)
GGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTG > SRR3722114.122835/1‑100 (MQ=60)
GGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTG > SRR3722114.160653/1‑100 (MQ=60)
GGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTG < SRR3722114.394209/100‑1 (MQ=60)
ATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAG > SRR3722114.402528/1‑100 (MQ=60)
GGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCctgtctctta > SRR3722114.59002/1‑90 (MQ=60)
GATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGG < SRR3722114.445829/100‑1 (MQ=60)
ATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGT > SRR3722114.166790/1‑100 (MQ=60)
CCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTGAACAGAGTCT > SRR3722114.277122/1‑100 (MQ=60)
|
CAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGAATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTGAACAGAGTCT > NZ_CP009273/1980343‑1980512
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
