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 |
2,648,012 |
C→T |
100% |
F140F (TTC→TTT) |
glgB → |
1,4‑alpha‑glucan branching enzyme |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,648,012 | 0 | C | T | 85.2%
| 64.0
/ 3.0
| 40 | F140F (TTC→TTT) | glgB | 1,4‑alpha‑glucan branching enzyme |
| Reads supporting (aligned to +/- strand): ref base C (2/4); new base T (9/25); total (11/29) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
| Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch. |
TGAAACCTTAGGCGCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTCTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCGGTGGTTGGGCAATTCA > minE/2647958‑2648061
|
tGAAACCTTAG‑‑GCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCaa < 1:1437540/69‑1 (MQ=255)
aaaCCTTAGGCGCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCaa < 1:831861/69‑1 (MQ=255)
aaaCCTTAGGCGCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCaa < 1:2266132/69‑1 (MQ=255)
aaaCCTTAGGCGCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCaa < 1:2131788/69‑1 (MQ=255)
aaaCCTTAGGCGCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCaa < 1:2645107/69‑1 (MQ=255)
aaaCCTTAGGCGCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCaa < 1:1876957/69‑1 (MQ=255)
aaaCCTTAGGCGCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCaa < 1:1718905/69‑1 (MQ=255)
aaaCCTTAGGCGCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCaa < 1:447045/69‑1 (MQ=255)
gcATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCgg > 1:3237339/1‑67 (MQ=255)
gcATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCgg > 1:3048323/1‑67 (MQ=255)
gcATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCgg > 1:3043477/1‑67 (MQ=255)
gcATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCgg > 1:1425345/1‑67 (MQ=255)
gcATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCgg > 1:2738924/1‑67 (MQ=255)
gcATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCgg > 1:473143/1‑67 (MQ=255)
gcATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCgg > 1:245735/1‑67 (MQ=255)
gcATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCgg > 1:764935/1‑67 (MQ=255)
gcATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCgg > 1:2388438/1‑67 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCTGGTCTCg < 1:1093628/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:2377093/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:510429/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:2041548/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:2625558/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:1986873/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:1468712/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:160216/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:155777/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:3053017/69‑1 (MQ=255)
gCAGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:3115193/69‑1 (MQ=255)
aGATACTATGGATGGCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:1357367/67‑1 (MQ=255)
gATACTATGGATGGCGTCACAGGTACGCGTTTCTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCggtg < 1:1195019/69‑1 (MQ=255)
gATACTATGGATGGCGTCACAGGTACGCGTTTCTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCggtg < 1:3202035/69‑1 (MQ=255)
atggatggCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:2348848/60‑1 (MQ=255)
tggatggCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:2246349/59‑1 (MQ=255)
tggatggCGTCACAGGTACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:2250273/59‑1 (MQ=255)
gCGTCAGAGGTACGCGTTTCTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCGGTGGTTGGGCAATTCa < 1:3022996/69‑1 (MQ=255)
gCGTCACAGGTACGCGTTTCTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCGGTGGTTGGGCAATTCa < 1:1545725/69‑1 (MQ=255)
tACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:3312262/43‑1 (MQ=255)
tACGCGTTTTTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCg < 1:1938938/43‑1 (MQ=255)
aCGCGTTTCTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCGGTGGTTGGGCAATTCa > 1:2547290/1‑58 (MQ=255)
aCGCGTTTCTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCGGTGGTTGGGCAATTCa > 1:1058565/1‑58 (MQ=255)
|
TGAAACCTTAGGCGCGCATGCAGATACTATGGATGGCGTCACAGGTACGCGTTTCTCTGTCTGGGCTCCAAACGCCCGTCGGGTCTCGGTGGTTGGGCAATTCA > minE/2647958‑2648061
|
| 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
