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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
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%
| 78.1
/ NA
| 22 | K330N (AAA→AAC) | glcA | glycolate permease GlcA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (6/16); total (6/16) |
GCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCA > NZ_CP009273/3113566‑3113728
|
gCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAAc < 1:87490/90‑1 (MQ=255)
gCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAAc < 1:75346/90‑1 (MQ=255)
cacTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCAt < 1:176760/90‑1 (MQ=255)
acTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATg < 2:188868/90‑1 (MQ=255)
ttgATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCa < 2:76769/90‑1 (MQ=255)
gCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATgg < 1:23440/90‑1 (MQ=255)
aaTGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGa > 1:346989/1‑90 (MQ=255)
tGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGAcc < 2:346989/90‑1 (MQ=255)
ggAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTa < 2:139230/90‑1 (MQ=255)
ccAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACg < 2:118104/90‑1 (MQ=255)
cAGTGAATAAACCGCGCCGCCCGGAGCAAATAACGCGTTAAACCGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACgg < 2:228218/90‑1 (MQ=255)
gAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGAc > 2:191424/1‑90 (MQ=255)
aTAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCa < 1:191424/90‑1 (MQ=255)
aaaCGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGc > 1:14922/1‑90 (MQ=255)
aaCGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCt > 2:145255/1‑90 (MQ=255)
cgccgcCCGGAGCAAATAACGCGTTAAACGGCTTCAt < 1:262662/37‑1 (MQ=38)
cgccgcCCGGAGCAAATAACGCGTTAAACGGCTTCAt > 2:262662/1‑37 (MQ=38)
cgccgcCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGaa > 1:158174/1‑90 (MQ=255)
cccGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGAtt < 2:347025/90‑1 (MQ=255)
aGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGccc < 2:14922/90‑1 (MQ=255)
aGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGccc < 2:337582/90‑1 (MQ=255)
cAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCa < 1:18622/90‑1 (MQ=255)
|
GCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCA > NZ_CP009273/3113566‑3113728
|
| 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
AATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTC > NZ_CP009273/3113556‑3113738
|
AATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAAC < SRR3722090.92656/100‑1 (MQ=60)
GCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGG < SRR3722090.76177/100‑1 (MQ=60)
GCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGG < SRR3722090.88449/100‑1 (MQ=60)
tgctcaggagtctcgtgggctcggagatgtgtataagagacagGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATG < SRR3722090.265890/57‑1 (MQ=60)
CACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATG < SRR3722090.178631/100‑1 (MQ=60)
TGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGA > SRR3722090.351504/1‑100 (MQ=60)
GCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCAC < SRR3722090.23690/100‑1 (MQ=60)
CCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGC > SRR3722090.15088/1‑100 (MQ=60)
GAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAA > SRR3722090.159770/1‑100 (MQ=60)
ATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATG < SRR3722090.193513/100‑1 (MQ=60)
CAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTC < SRR3722090.18826/100‑1 (MQ=60)
|
AATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTC > NZ_CP009273/3113556‑3113738
|
| 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: ‑ |
