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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,854,126 |
T→C |
M121V (ATG→GTG) |
ydjK ← |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,854,126 | 0 | T | C | 100.0%
| 104.8
/ NA
| 30 | M121V (ATG→GTG) | ydjK | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/19); total (11/19) |
TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCAT > NZ_CP009273/1854049‑1854206
|
tCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggca < 1:273113/90‑1 (MQ=255)
gATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCaa < 2:195054/90‑1 (MQ=255)
tCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAg > 1:618472/1‑90 (MQ=255)
cTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAgg < 1:758391/90‑1 (MQ=255)
tACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGa < 2:475902/90‑1 (MQ=255)
aCCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGaa < 1:330612/90‑1 (MQ=255)
aCCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGaa < 1:846760/90‑1 (MQ=255)
gggCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGTCAGGCAATAAGGAAATc > 1:619782/1‑90 (MQ=255)
gggCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATc > 2:748997/1‑90 (MQ=255)
tatatTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCatat < 1:830757/90‑1 (MQ=255)
ggTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTga > 1:196817/1‑90 (MQ=255)
aaaCCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGaaa > 1:129550/1‑90 (MQ=255)
aaaCCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGaaa > 1:283357/1‑90 (MQ=255)
aCCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGc < 1:78599/90‑1 (MQ=255)
cAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAAc > 1:535434/1‑90 (MQ=255)
gCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCa > 2:706027/1‑90 (MQ=255)
tAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCg < 1:83165/90‑1 (MQ=255)
cAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGc < 1:422787/90‑1 (MQ=255)
aGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCa > 2:721578/1‑90 (MQ=255)
tAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAat < 1:721578/90‑1 (MQ=255)
tAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAat > 1:689947/1‑90 (MQ=255)
tAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAat < 2:689947/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt > 1:659693/1‑90 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 1:521566/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 2:207185/90‑1 (MQ=255)
cccAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATg < 1:273486/90‑1 (MQ=255)
aGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 2:854465/90‑1 (MQ=255)
aGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 2:208257/90‑1 (MQ=255)
aGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 1:547879/90‑1 (MQ=255)
cAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCAt < 1:136888/90‑1 (MQ=255)
|
TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCAT > NZ_CP009273/1854049‑1854206
|
| 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
AAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAA > NZ_CP009273/1854030‑1854216
|
AAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCAC < SRR3722072.6038/100‑1 (MQ=60)
TTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAG > SRR3722072.629509/1‑100 (MQ=60)
TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGG < SRR3722072.277780/100‑1 (MQ=60)
GATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGTCAGGCAATAAGGAAATC > SRR3722072.630842/1‑100 (MQ=60)
CTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATAT < SRR3722072.771769/100‑1 (MQ=60)
ACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTC < SRR3722072.861403/100‑1 (MQ=60)
ACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTC < SRR3722072.336417/100‑1 (MQ=60)
GCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGA > SRR3722072.200211/1‑100 (MQ=60)
TATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAA < SRR3722072.845174/100‑1 (MQ=60)
ATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAA > SRR3722072.131887/1‑100 (MQ=60)
ATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAA > SRR3722072.288209/1‑100 (MQ=60)
AACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAAC > SRR3722072.545079/1‑100 (MQ=60)
ACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACC < SRR3722072.80058/100‑1 (MQ=60)
GCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAAT > SRR3722072.702286/1‑100 (MQ=60)
TAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATG < SRR3722072.84725/100‑1 (MQ=60)
CCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGctgtctcttatacacatctccgagcccacgagacgtccgattatctcgtat > SRR3722072.81649/1‑49 (MQ=60)
CCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAT > SRR3722072.671464/1‑100 (MQ=60)
CAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATG < SRR3722072.430470/100‑1 (MQ=60)
TAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCC < SRR3722072.734413/100‑1 (MQ=60)
TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATNG < SRR3722072.639406/100‑1 (MQ=60)
TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG < SRR3722072.530950/100‑1 (MQ=60)
CCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGA < SRR3722072.278160/100‑1 (MQ=60)
AGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGA < SRR3722072.557728/100‑1 (MQ=60)
CAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAA < SRR3722072.139331/100‑1 (MQ=60)
|
AAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAA > NZ_CP009273/1854030‑1854216
|
| 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: ‑ |
