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 |
886,189 |
A→G |
G7G (GGT→GGC) |
grxA ← |
glutaredoxin 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 886,189 | 0 | A | G | 100.0%
| 50.8
/ NA
| 15 | G7G (GGT→GGC) | grxA | glutaredoxin 1 |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (7/8); total (7/8) |
TACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGT > NZ_CP009273/886106‑886270
|
tactgatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCaaaa > 2:125580/1‑90 (MQ=255)
tactgatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCaaaa > 2:59795/1‑90 (MQ=255)
ctgatactgaAAATCATCGCGTCCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAAt > 2:143312/1‑90 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa < 1:32519/90‑1 (MQ=255)
actgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACgg < 2:3625/90‑1 (MQ=255)
aaaTCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGc > 1:147046/1‑90 (MQ=255)
gTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTtctc < 1:44802/90‑1 (MQ=255)
cTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATa < 2:23984/90‑1 (MQ=255)
tctcAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTAt < 1:259729/90‑1 (MQ=255)
cAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGcc < 1:125580/90‑1 (MQ=255)
tttGCACGCACCCAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCa < 2:167052/90‑1 (MQ=255)
gggCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCt > 1:120316/1‑90 (MQ=255)
gCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGa > 1:104485/1‑90 (MQ=255)
gCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGa > 2:69207/1‑90 (MQ=255)
cccGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGt < 1:257716/90‑1 (MQ=255)
|
TACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGT > NZ_CP009273/886106‑886270
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGTAGGTTTAACC > NZ_CP009273/886108‑886280
|
CTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGC > SRR3722090.148565/1‑100 (MQ=60)
GATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCAT < SRR3722090.32841/100‑1 (MQ=60)
GTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGA < SRR3722090.45264/100‑1 (MQ=60)
TCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATG < SRR3722090.262922/100‑1 (MQ=60)
CAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATC < SRR3722090.126908/100‑1 (MQ=60)
CACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCT > SRR3722090.121592/1‑100 (MQ=60)
CACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGA > SRR3722090.105608/1‑100 (MQ=60)
CAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCctgtctcttatacacatctccgagcccacgagactcctgagcatctcgtatgc > SRR3722090.130343/1‑47 (MQ=60)
CCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGTAGGTTTAACC < SRR3722090.260872/100‑1 (MQ=60)
|
CTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGTAGGTTTAACC > NZ_CP009273/886108‑886280
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
