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 |
|
A1 F21 I0 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,714,423 |
C→T |
40.9% |
H61Y (CAC→TAC) |
atpI → |
ATP synthase, membrane‑bound accesory subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,714,423 | 0 | C | T | 40.9%
| 10.8
/ 22.1
| 22 | H61Y (CAC→TAC) | atpI | ATP synthase, membrane‑bound accesory subunit |
| Reads supporting (aligned to +/- strand): ref base C (11/2); new base T (3/6); total (14/8) |
| Fisher's exact test for biased strand distribution p-value = 2.60e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTT > W3110S.gb/3714366‑3714483
|
aGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATa < 1:585556/70‑1 (MQ=255)
aGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATa > 1:198864/1‑70 (MQ=255)
ccTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCg > 1:952826/1‑70 (MQ=255)
ccTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCg > 1:1415966/1‑70 (MQ=255)
ccTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCg > 1:673232/1‑70 (MQ=255)
tGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:1244104/58‑1 (MQ=255)
tGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:786589/58‑1 (MQ=255)
tGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:688626/58‑1 (MQ=255)
tGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:193079/58‑1 (MQ=255)
tGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:1767977/58‑1 (MQ=255)
tGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:1629936/58‑1 (MQ=255)
tGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa < 1:446225/58‑1 (MQ=255)
gTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCg > 1:1438533/1‑71 (MQ=255)
gTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCg > 1:1322134/1‑71 (MQ=255)
gTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCg > 1:1075709/1‑71 (MQ=255)
tGCCTGGCGTCACCAGGCGCATACCCCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt > 1:795389/1‑71 (MQ=255)
tGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt > 1:1682807/1‑71 (MQ=255)
tGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt > 1:1316200/1‑71 (MQ=255)
tGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt > 1:789424/1‑71 (MQ=255)
tGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt > 1:80512/1‑71 (MQ=255)
tGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt > 1:816035/1‑71 (MQ=255)
tGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt > 1:908745/1‑71 (MQ=255)
|
AGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTT > W3110S.gb/3714366‑3714483
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
