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 |
2,654,894 |
A→C |
54.4% |
G127G (GGA→GGC) |
glgP → |
glycogen phosphorylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,654,894 | 0 | A | C | 54.4%
| 15.3
/ 43.3
| 46 | G127G (GGA→GGC) | glgP | glycogen phosphorylase |
| Reads supporting (aligned to +/- strand): ref base A (19/2); new base C (6/19); total (25/21) |
| Fisher's exact test for biased strand distribution p-value = 5.97e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01 |
GGGGTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCTTGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTACGGCATCC > minE/2654828‑2654961
|
gggaTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCGGGCCTCGGTAACGGTGGCCTGGGCCg < 1:588092/69‑1 (MQ=255)
gggaTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCGGGCCTCGGTAACGGTGGCCTGGGCCg < 1:3429460/69‑1 (MQ=255)
gggaTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCGGGCCTCGGTAACGGTGGCCTGGGCCg < 1:2999791/69‑1 (MQ=255)
gggaTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCGGGCCTCGGTAACGGTGGCCTGGGCCg < 1:1671746/69‑1 (MQ=255)
gggaTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCGGGCCTCGGTAACGGTGGCCTGGGCCg < 1:2474231/69‑1 (MQ=255)
gggaTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCGGGCCTCGGTAACGGTGGCCTGGGCCg < 1:2117678/69‑1 (MQ=255)
gggaTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCGGGCCTCGGTAACGGTGGCCTGGGCCg < 1:1809051/69‑1 (MQ=255)
gggaTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCGGGCCTCGGTAACGGTGGCCTGGGCCg < 1:2038517/69‑1 (MQ=255)
gggTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGt > 1:488907/1‑69 (MQ=255)
gTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCt > 1:457190/1‑69 (MQ=255)
aaaTCTCGAAGAGCTGATTGATGAAGAAAATGACCCGGGCCTCGGTAACGGTGGCCTGGGCCg < 1:1458807/63‑1 (MQ=255)
aaaTCTCGAAGAGCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTggc > 1:527665/1‑69 (MQ=255)
aaaTCTCGAAGAGCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTggc > 1:1360571/1‑69 (MQ=255)
aaaTCTCGAAGAGCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTggc > 1:1812126/1‑69 (MQ=255)
aaaTCTCGAAGAGCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTgg > 1:887319/1‑68 (MQ=255)
agagCTGATTGATCAAGAAAATGACCCAGGCCGCGGTAACGGTGGCCTGGGACGTCTGGCGgcttgc < 1:3229975/67‑1 (MQ=255)
gagCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTc > 1:1799556/1‑69 (MQ=255)
gagCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTc > 1:3141445/1‑69 (MQ=255)
gagCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTc > 1:1795544/1‑69 (MQ=255)
gagCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTc > 1:2970190/1‑69 (MQ=255)
cTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCtt > 1:2222656/1‑69 (MQ=255)
gattgatGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCTTGa > 1:3098344/1‑69 (MQ=255)
aagaaAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCTTGGTtc > 1:1883332/1‑64 (MQ=255)
aagaaAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCTTGATtc > 1:1087493/1‑64 (MQ=255)
aagaaAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCTTGATtc > 1:731000/1‑64 (MQ=255)
aagaaAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCTTGATtc > 1:658187/1‑64 (MQ=255)
aagaaAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCTTGATtc > 1:259334/1‑64 (MQ=255)
aagaaAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCTTGATtc > 1:2864750/1‑64 (MQ=255)
aagaaAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTATGGCGGCTTGCTTCCTTGATtc > 1:3033408/1‑64 (MQ=255)
aaaaTGACCCAGGCCTCGGTATCGGGGGCCTGGGACGTCTGGCGgcttgc < 1:84324/50‑1 (MQ=37)
tGGCCTGGGCCGTGTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:1646214/69‑1 (MQ=38)
tGGCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:1398148/69‑1 (MQ=255)
tGGCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:2120900/69‑1 (MQ=255)
tGGCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:411679/69‑1 (MQ=255)
tGGCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:2192441/69‑1 (MQ=255)
tGGCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:2525236/69‑1 (MQ=255)
tGGCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:2552258/69‑1 (MQ=255)
tGGCCTGGGCCGTCTGGCGGCTTGCTTCATCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:848624/69‑1 (MQ=38)
ggCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAggg > 1:3359581/1‑51 (MQ=255)
ggCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAggg > 1:1500034/1‑51 (MQ=255)
ggCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAggg > 1:2432437/1‑51 (MQ=255)
ggCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAggg > 1:1369959/1‑51 (MQ=255)
ggCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAggg > 1:1163988/1‑51 (MQ=255)
ggCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAggg > 1:1992017/1‑51 (MQ=255)
ggCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:1207158/68‑1 (MQ=255)
ggCCTGGGCCGTCTGGCGGCTTGCTTCCTCGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTa < 1:1863303/68‑1 (MQ=255)
aCGTCTGGCGGCTTGCTTCCTTGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTACGGCATcc > 1:2713950/1‑68 (MQ=255)
|
GGGGTTAAATCTCGAAGAGCTGATTGATGAAGAAAATGACCCAGGCCTCGGTAACGGTGGCCTGGGACGTCTGGCGGCTTGCTTCCTTGATTCTCTGGCGACGTTAGGGTTGCCGGGGCGCGGTTACGGCATCC > minE/2654828‑2654961
|
| 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
