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 |
1,062,210 |
T→C |
G390G (GGT→GGC) |
agp → |
bifunctional glucose‑1‑phosphatase/inositol phosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,062,210 | 0 | T | C | 100.0%
| 30.8
/ NA
| 10 | G390G (GGT→GGC) | agp | bifunctional glucose‑1‑phosphatase/inositol phosphatase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/5); total (5/5) |
TGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGTTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAG > NZ_CP009273/1062135‑1062249
|
tGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGc > 2:331766/1‑90 (MQ=255)
aTGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGa > 1:208482/1‑90 (MQ=255)
aTGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGa > 2:55389/1‑90 (MQ=255)
aTGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa < 1:341094/90‑1 (MQ=255)
aTGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa > 2:133491/1‑90 (MQ=255)
aTGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa < 2:208482/90‑1 (MQ=255)
aTGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa < 2:302364/90‑1 (MQ=255)
gCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAg < 1:298595/90‑1 (MQ=255)
gtgtGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa > 1:14137/1‑60 (MQ=255)
gtgtGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATa < 2:14137/60‑1 (MQ=255)
|
TGCGGAACAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGTTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAG > NZ_CP009273/1062135‑1062249
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
CAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGTTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGA > NZ_CP009273/1062142‑1062277
|
CAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGA > SRR3722090.210798/1‑100 (MQ=60)
ATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAG < SRR3722090.345534/100‑1 (MQ=60)
GCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCG < SRR3722090.302375/100‑1 (MQ=60)
CCTGCGCAGCGTGTGACGCTGGAATTAAGCGGCTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCtgtctcttatacacatctc > SRR3722090.14288/1‑81 (MQ=60)
|
CAGTTACGTAATGCCGATGCGTTAACCCTGCAGGCACCTGCGCAGCGTGTGACGCTGGAATTAAGCGGTTGCCCGATAGACGCTGATGGTTTCTGCCCGATGGATAAGTTTGATAGCGTGTTGAATGAAGCGGTGA > NZ_CP009273/1062142‑1062277
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
