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 |
1,017,325 |
G→T |
100% |
W353C (TGG→TGT) |
manA → |
mannose‑6‑phosphate isomerase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,017,325 | 0 | G | T | 85.1%
| 130.7
/ 16.2
| 67 | W353C (TGG→TGT) | manA | mannose‑6‑phosphate isomerase |
| Reads supporting (aligned to +/- strand): ref base G (10/0); new base T (41/16); total (51/16) |
| Fisher's exact test for biased strand distribution p-value = 1.02e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.74e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ACCATTAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGT > minE/1017266‑1017393
|
accaTCAGCCAGCAGAGTGCCTCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:3185909/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:1086144/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:2065535/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:2141680/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:2198716/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:2290361/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:2628497/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:1462394/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:274915/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:2821634/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:3010770/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:3147641/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:671625/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGtt > 1:1114126/1‑67 (MQ=255)
accaTCAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGt > 1:2568952/1‑66 (MQ=255)
ttAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTcagc > 1:2045819/1‑69 (MQ=255)
ttAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTcagc > 1:3039201/1‑69 (MQ=255)
ttAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTcagc > 1:301578/1‑69 (MQ=255)
ttAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTcagc > 1:2312722/1‑69 (MQ=255)
ttAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTcagc > 1:1659852/1‑69 (MQ=255)
ttAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTcagc > 1:378741/1‑69 (MQ=255)
ttAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTcag > 1:1488524/1‑68 (MQ=255)
ttAGCCAGCAGAGTGCCGCCATTTCGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTcagc > 1:1319895/1‑69 (MQ=255)
gccATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACATCTTAAACCg > 1:3413459/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTa > 1:2311150/1‑59 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTg > 1:234609/1‑68 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTg > 1:2252072/1‑68 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTg > 1:285073/1‑68 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTg > 1:1115681/1‑68 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTg > 1:1936795/1‑68 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:3329352/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:1391412/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:1371857/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:2955101/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:1346987/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:1341095/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:3086596/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:3122922/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:1232774/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:3153135/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:1169424/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:1941737/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:3342622/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:3431737/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:405142/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:471526/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:553551/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:587199/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:591498/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:689961/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:1545209/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:1728747/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:2221328/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:2124365/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:2086501/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:2028725/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:1643585/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:1572901/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:2354427/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:1524096/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:2611612/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa < 1:1503532/69‑1 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:2634463/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:2654644/1‑69 (MQ=255)
tttGTTCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGCTGa > 1:1412216/1‑69 (MQ=255)
tttGTCCTGCGTCGAAGGCGATGCAACGCTGTGTAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGa > 1:1362445/1‑69 (MQ=255)
gCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCaa > 1:2796289/1‑68 (MQ=255)
gAAAGTTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCTGt < 1:1161859/69‑1 (MQ=255)
gAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGt < 1:983497/69‑1 (MQ=255)
gAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGt < 1:2131475/69‑1 (MQ=255)
gAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGt < 1:2163893/69‑1 (MQ=255)
gAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGt < 1:1117972/69‑1 (MQ=255)
gAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGt < 1:2249608/69‑1 (MQ=255)
gAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGt < 1:33445/69‑1 (MQ=255)
gAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGt < 1:105661/69‑1 (MQ=255)
gAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGt < 1:1706581/69‑1 (MQ=255)
gAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGt < 1:2698759/69‑1 (MQ=255)
|
ACCATTAGCCAGCAGAGTGCCGCCATTTTGTTCTGCGTCGAAGGCGATGCAACGTTGTGGAAAGGTTCTCAGCAGTTACAGCTTAAACCGGGTGAATCAGCGTTTATTGCCGCCAACGAATCACCGGT > minE/1017266‑1017393
|
| 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
