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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
267,498 |
A→T |
62.5% |
G383G (GGT→GGA) |
dxs ← |
1‑deoxyxylulose‑5‑phosphate synthase, thiamine‑requiring, FAD‑requiring |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 267,498 | 0 | A | T | 62.5%
| 38.7
/ 46.2
| 56 | G383G (GGT→GGA) | dxs | 1‑deoxyxylulose‑5‑phosphate synthase, thiamine‑requiring, FAD‑requiring |
| Reads supporting (aligned to +/- strand): ref base A (5/16); new base T (11/24); total (16/40) |
| Fisher's exact test for biased strand distribution p-value = 7.61e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CACCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGT > minE/267438‑267559
|
caCCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGc < 1:823779/69‑1 (MQ=255)
caCCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGc < 1:20259/69‑1 (MQ=255)
aCCTGATCATAGGCGCGTTTCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1432310/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGcctcc > 1:396958/1‑62 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1270586/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:2337692/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:2208084/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:432012/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:193886/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1897281/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1875378/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:717394/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1475585/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCCCAACAATGGGTTTGTAGCCTCCAATc > 1:2351589/1‑66 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:200264/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:157190/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:90811/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:3206777/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:3110022/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:2321842/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:1226057/68‑1 (MQ=255)
gcgTTGCAGGAAGGTGGAGTAGATCGCAACAATCGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:2828582/67‑1 (MQ=255)
gcgACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTc > 1:941351/1‑62 (MQ=255)
gcgACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAAtt > 1:336637/1‑69 (MQ=255)
gcgACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAAtt > 1:2825384/1‑69 (MQ=255)
gcgACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAAtt > 1:3047174/1‑69 (MQ=255)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:2739202/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:972663/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:903998/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:898411/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:859296/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:1630551/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:551414/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:5159/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:487139/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:206805/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:267183/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:2550390/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:3217225/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:3116811/39‑1 (MQ=37)
caaCAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:2213252/39‑1 (MQ=37)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:631388/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:2713938/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:1471804/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:898449/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:1563765/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:779599/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:2321110/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:503629/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:2052206/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:412341/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:378941/69‑1 (MQ=255)
cAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:377679/69‑1 (MQ=255)
cAATGGGTTTGTAACCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:2437525/69‑1 (MQ=255)
aaTGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCa < 1:3350616/68‑1 (MQ=255)
tGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:2291536/35‑1 (MQ=25)
tGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGt > 1:1442716/1‑69 (MQ=255)
|
CACCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATTGCCACGTCGAAGT > minE/267438‑267559
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
