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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,113,649 |
T→G |
K330N (AAA→AAC) |
glcA ← |
glycolate permease GlcA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,113,649 | 0 | T | G | 100.0%
| 74.9
/ NA
| 24 | K330N (AAA→AAC) | glcA | glycolate permease GlcA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (7/17); total (7/17) |
CCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCA > NZ_CP009273/3113564‑3113728
|
ccGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTaa > 1:164940/1‑90 (MQ=255)
gCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAAc < 1:251918/90‑1 (MQ=255)
cacTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCAt < 1:567848/90‑1 (MQ=255)
cacTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCAt < 1:569164/90‑1 (MQ=255)
acTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATg < 2:534872/90‑1 (MQ=255)
acTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATg < 1:67369/90‑1 (MQ=255)
acTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATg < 2:243353/90‑1 (MQ=255)
gttgATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTcc < 1:346774/90‑1 (MQ=255)
aTGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGAt > 2:111981/1‑90 (MQ=255)
gCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATgg < 1:414870/90‑1 (MQ=255)
gCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATgg < 1:144802/90‑1 (MQ=255)
tGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGAcc < 1:397783/90‑1 (MQ=255)
gAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCa < 1:527427/90‑1 (MQ=255)
gggATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGc > 2:628958/1‑90 (MQ=255)
gATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCAc > 2:496269/1‑90 (MQ=255)
gATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCAc < 2:164940/90‑1 (MQ=255)
ggAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTa > 1:377043/1‑90 (MQ=255)
ggAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTa < 2:377043/90‑1 (MQ=255)
cAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACgg < 1:237816/90‑1 (MQ=255)
aaTAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGAcc < 1:440747/90‑1 (MQ=255)
aTAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCa < 1:480776/90‑1 (MQ=255)
gccgccCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAAt > 1:423491/1‑90 (MQ=255)
aGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGccc > 1:76490/1‑90 (MQ=255)
cAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCa < 2:76490/90‑1 (MQ=255)
|
CCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCA > NZ_CP009273/3113564‑3113728
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
ACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTCTG > NZ_CP009273/3113554‑3113740
|
ACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAA > SRR3722088.166607/1‑100 (MQ=60)
TGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGG < SRR3722088.247107/100‑1 (MQ=60)
GCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGG < SRR3722088.254376/100‑1 (MQ=60)
TTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTgtctcttatacacatctc > SRR3722088.145688/1‑82 (MQ=60)
CACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATG < SRR3722088.576139/100‑1 (MQ=60)
CACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATG < SRR3722088.574814/100‑1 (MQ=60)
ACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGG < SRR3722088.68070/100‑1 (MQ=60)
GTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGAC < SRR3722088.350425/100‑1 (MQ=60)
GCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCAC < SRR3722088.146280/100‑1 (MQ=60)
GCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCAC < SRR3722088.419462/100‑1 (MQ=60)
TGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTA < SRR3722088.402086/100‑1 (MQ=60)
TGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTA > SRR3722088.381054/1‑100 (MQ=60)
GAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAA < SRR3722088.533822/100‑1 (MQ=60)
CAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCT < SRR3722088.240167/100‑1 (MQ=60)
AATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAAT > SRR3722088.428236/1‑100 (MQ=60)
AATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAAT < SRR3722088.445821/100‑1 (MQ=60)
ATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATG < SRR3722088.486500/100‑1 (MQ=60)
CGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCC > SRR3722088.77267/1‑100 (MQ=60)
GAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATA > SRR3722088.415642/1‑100 (MQ=60)
AAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATA‑TCTG > SRR3722088.487555/1‑100 (MQ=60)
|
ACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTCTG > NZ_CP009273/3113554‑3113740
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
