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 |
2,512,485 |
C→T |
60.5% |
A15A (GCG→GCA) |
yicE ← |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,512,485 | 0 | C | T | 60.5%
| 14.7
/ 27.5
| 43 | A15A (GCG→GCA) | yicE | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base C (4/13); new base T (8/18); total (12/31) |
| Fisher's exact test for biased strand distribution p-value = 7.35e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGGGTTTGAGGAAGCGGCGGACGATCTTCAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTGG > minE/2512422‑2512546
|
cAGGGTTTGAGGAAGCGGCGGACGATCTTCAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGCGCAAc < 1:1289160/69‑1 (MQ=255)
cAGGGTTTGAGGAAGCGGCGGACGATCTTCAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGCGCAAc < 1:146225/69‑1 (MQ=255)
cAGGGTTTGAGGAAGCGGCGGACGATCTTCAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGCGCAAc < 1:2550386/69‑1 (MQ=255)
cAGGGTTTGAGGAAGCGGCGGACGATCTTCAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGCGCAAc > 1:2223346/1‑69 (MQ=255)
gTTTGAGGAAGAGGCGGACGATCTTCAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGCGCAACGGGt > 1:2736378/1‑69 (MQ=255)
aTCTTCAAGACGGTAAATCAGTGCGCTGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTTACTCGAg < 1:796563/69‑1 (MQ=255)
cAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGTGCAACCGGTTGCGCAtt > 1:3151780/1‑52 (MQ=255)
cAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTg > 1:967484/1‑68 (MQ=255)
cAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTg > 1:939629/1‑68 (MQ=255)
cAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTg > 1:652660/1‑68 (MQ=255)
cAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTg > 1:3080482/1‑68 (MQ=255)
cAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTg > 1:2826369/1‑68 (MQ=255)
cAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTg > 1:1526151/1‑68 (MQ=255)
cAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTg > 1:1987121/1‑68 (MQ=255)
cGGTAAATCAGTTCGCTGTTTTGAGTCTGCGCAACCggg > 1:328350/1‑38 (MQ=255)
tCAGTTCGCTGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTc < 1:3203120/49‑1 (MQ=255)
tCAGTTCGCTGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACa < 1:2277017/62‑1 (MQ=255)
tCAGTTCGCTGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACa < 1:2363166/62‑1 (MQ=255)
tCAGTTCGCTGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACa < 1:2788842/62‑1 (MQ=255)
cGCTGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACa < 1:1320844/56‑1 (MQ=255)
tGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAAt < 1:175425/68‑1 (MQ=255)
tGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAAt < 1:1456065/68‑1 (MQ=255)
gTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAAt < 1:2925955/67‑1 (MQ=255)
ttGAGTCTGCGCCACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACa > 1:259554/1‑49 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:3307601/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:2992261/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:3366625/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:641031/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:684415/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:717760/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:75955/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:1255044/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:1101623/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:3303622/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:1538139/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:2918091/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:1669774/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:2815738/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:1786510/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:2523912/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:2377841/68‑1 (MQ=255)
aGTCTGTGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTgg < 1:1909724/68‑1 (MQ=255)
tGCGCAACCGGTTGCGCATTTTCTGACTCGTGGGTGGAAACa < 1:2487904/42‑1 (MQ=255)
|
CAGGGTTTGAGGAAGCGGCGGACGATCTTCAAGACGGTAAATCAGTTCGCTGTTTTGAGTCTGCGCAACCGGTTGCGCATTTTCTGACTCGAGGGTGGAAACAGACATCGAAAACAATCCCGTGG > minE/2512422‑2512546
|
| 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
