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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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 | 92.9%
| 36.1
/ ‑4.4
| 14 | G7G (GGT→GGC) | grxA | glutaredoxin 1 |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (10/3); total (10/4) |
| Fisher's exact test for biased strand distribution p-value = 2.86e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAA > NZ_CP009273/886104‑886268
|
cATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCaa > 2:393609/1‑90 (MQ=255)
actgatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCaaaaa > 2:110612/1‑90 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa > 2:262465/1‑90 (MQ=255)
cgTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCACTATTtct < 1:475572/90‑1 (MQ=255)
ttGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTctcctc > 1:327486/1‑90 (MQ=255)
tctcAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTAt < 1:417468/90‑1 (MQ=255)
ttttGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATc < 2:179959/90‑1 (MQ=255)
acgcacACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTa > 1:53593/1‑90 (MQ=255)
ggCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTg < 2:238782/90‑1 (MQ=255)
aaCCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGaaa > 1:264558/1‑90 (MQ=255)
aaCCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGaaa > 1:413941/1‑90 (MQ=255)
aaCCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGaaa > 1:61881/1‑90 (MQ=255)
aaCCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGaaa > 2:338586/1‑90 (MQ=255)
aaCCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGaaa > 2:93719/1‑90 (MQ=255)
|
CATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAA > NZ_CP009273/886104‑886268
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
ATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGTAGGTTTAACC > NZ_CP009273/886123‑886280
|
ATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTC > SRR3722094.332805/1‑100 (MQ=60)
CGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCACTATTTCTCTCCTCATAG < SRR3722094.483975/100‑1 (MQ=60)
TCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATG < SRR3722094.424740/100‑1 (MQ=60)
GATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTA > SRR3722094.54337/1‑100 (MQ=60)
CAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAA > SRR3722094.268494/1‑100 (MQ=60)
CAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAA > SRR3722094.421146/1‑100 (MQ=60)
CAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAA > SRR3722094.62744/1‑100 (MQ=60)
CCCGAACAGCCAAAAATAACGGTTTGCATTATTCCTCTCCTCATAGATTTATGCCTGTAATGATCACGATAAAATGTATTCGCTGAAAGTAGTTTTAACC < SRR3722094.229943/100‑1 (MQ=60)
|
ATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGTAGGTTTAACC > NZ_CP009273/886123‑886280
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
