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 |
974,805 |
G→T |
56.2% |
intergenic (+557/+435) |
lsrB → / ← ydeH |
AI2 transporter/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 974,805 | 0 | G | T | 56.2%
| 3.3
/ 50.9
| 48 | intergenic (+557/+435) | lsrB/ydeH | AI2 transporter/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (10/11); new base T (8/19); total (18/30) |
| Fisher's exact test for biased strand distribution p-value = 2.40e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACATTTTGTTCGTCAATAAACATGCAGCGATTTCTTCCGGTTTGCTTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGAAATGCGCGACTCACACCTGC > minE/974741‑974865
|
acaTTTTGTTCGTCAATAAACATGCAGCGATTTCTTCCGGTTTGCTTACCCTCATACATTGCCCGGTcc > 1:3158191/1‑69 (MQ=255)
aaTAAACATGCAGCGATTTCTTCCGGTTTGCTTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGAc > 1:1883172/1‑69 (MQ=255)
aaCATGCAGCGATTTCTTCCGGTTTGCTTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGACcaca > 1:2351791/1‑69 (MQ=255)
aaCATGCAGCGATTTCTTCCGGTTTGCTTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGACcaca > 1:776604/1‑69 (MQ=255)
aaCATGCAGCGATTTCTTCCGGTTTGCTTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGACcaca > 1:547189/1‑69 (MQ=255)
cATGCAGCGATTTCTTCCGGTTTGCTTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGACcaca > 1:2391757/1‑67 (MQ=255)
aGCGATTCCTTCCGGTTTGCTTACCCTCATACATTGCCCTGTCCGCTCTTCCAATGACcac > 1:2620340/1‑61 (MQ=255)
aGCGATTCCTTCCGGTTTGCTTACCCTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCagag > 1:883488/1‑69 (MQ=255)
aGCGATTCCTTCCGGTTTGCTTACCCTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCagag > 1:2425781/1‑69 (MQ=255)
aGCGATTCCTTCCGGTTTGCTTACCCTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCagag > 1:3428549/1‑69 (MQ=255)
aGCGATTCCTTCCGGTTTGCTTACCCTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCagag > 1:1648580/1‑69 (MQ=255)
aGCGATTCCTTCCGGTTTGCTTACCCTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCagag > 1:1639095/1‑69 (MQ=255)
aGCGATTCCTTCCGGTTTGCTTACCCTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCagag > 1:788563/1‑69 (MQ=255)
aGCGATTCCTTCCGGTTTGCTTACCCTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCagag > 1:1162221/1‑69 (MQ=255)
gCGATTTCTTCCGGTTTGCTTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGACCACATCCAGAgg < 1:431853/69‑1 (MQ=255)
gCGATTTCTTCCGGTTTGCGTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGACCACATCCAGAgg < 1:1446844/69‑1 (MQ=255)
gCGATTTCTTCCGGGTTGCTTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGACCACATCCAGAgg < 1:486994/69‑1 (MQ=255)
tcttcCGGTTTGCTTACCCTCATACATTGCCCGGTCCGc < 1:3324687/39‑1 (MQ=255)
tcttcCGGTTTGCTTACCCTCATACATTGCCCGGTCCGc < 1:3295447/39‑1 (MQ=255)
tcttcCGGTTTGCTTACCCTCATACATTGCCCGGTCCGc < 1:1131990/39‑1 (MQ=255)
tcttcCGGTTTGCTTACCCTCATACATTGCCCGGTCCGc < 1:1316793/39‑1 (MQ=255)
tcttcCGGTTTGCTTACCCTCATACATTGCCCGGTCCGc < 1:171564/39‑1 (MQ=255)
tcttcCGGTTTGCTTACCCTCATACATTGCCCGGTCCGc < 1:2192544/39‑1 (MQ=255)
tcttcCGGTTTGCTTACCCTCATACATTGCCCGGTCCGc < 1:1743673/39‑1 (MQ=255)
cttcCGGTTTGCTTACCCTCATACATTGCCCGGTCCGc < 1:708521/38‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:3385919/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:1029223/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:769161/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:568263/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:157700/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:521988/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:424698/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:3407389/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:3381803/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:1775010/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:3122170/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:2983806/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:2892199/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:2212032/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:2573606/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:2509560/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:2505115/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGa < 1:2325914/57‑1 (MQ=255)
cccTCATACATTGCCCTGTCCGCTCTTCCAATGACCACATCC‑‑AGGCTCTTCAGGa < 1:257756/55‑1 (MQ=255)
cATTGCCCGGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGAAATGCGCGACTCACACctgc > 1:2366667/1‑69 (MQ=255)
cATTGCCCGGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGAAATGCGCGACTCACACctgc > 1:1717848/1‑69 (MQ=255)
cATTGCCCGGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGAAATGCGCGACTCACACctg > 1:1209632/1‑68 (MQ=255)
cATTGACCGGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGAAATGCGCGACTCACACctgc > 1:1796461/1‑69 (MQ=255)
|
ACATTTTGTTCGTCAATAAACATGCAGCGATTTCTTCCGGTTTGCTTACCCTCATACATTGCCCGGTCCGCTCTTCCAATGACCACATCCAGAGGCTCTTCAGGAAATGCGCGACTCACACCTGC > minE/974741‑974865
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
