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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,657,562 |
T→C |
100% |
I14T (ATT→ACT) |
ynfB → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,657,562 | 0 | T | C | 84.2%
| 94.7
/ 10.3
| 38 | I14T (ATT→ACT) | ynfB | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (1/5); new base C (8/24); total (9/29) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATT > W3110S.gb/1657497‑1657626
|
tAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTActct < 1:976394/69‑1 (MQ=255)
tAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTActct < 1:3323111/69‑1 (MQ=255)
tAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTActct < 1:3319826/69‑1 (MQ=255)
tAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTctg < 1:1190392/70‑1 (MQ=255)
attcatACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCTGCCTGCTCGCTACTCTGCTGCCt > 1:1903985/1‑71 (MQ=255)
attcatACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCt > 1:735684/1‑71 (MQ=255)
gggAATTAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTgcg < 1:228190/66‑1 (MQ=255)
tgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCAtt > 1:2892875/1‑71 (MQ=255)
tgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCAtt > 1:2058065/1‑71 (MQ=255)
tgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCAt > 1:2801943/1‑70 (MQ=255)
aatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCtgctgc > 1:2655673/1‑53 (MQ=255)
tGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGcac < 1:3310276/70‑1 (MQ=255)
tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:1700351/71‑1 (MQ=255)
tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:1817852/71‑1 (MQ=255)
tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:1963669/71‑1 (MQ=255)
tCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:2088759/71‑1 (MQ=255)
aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTg < 1:3651712/61‑1 (MQ=255)
aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTg < 1:1980061/61‑1 (MQ=255)
aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTg < 1:1809996/61‑1 (MQ=255)
aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTg < 1:1725918/61‑1 (MQ=255)
aGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa < 1:214374/71‑1 (MQ=255)
gCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTg < 1:2295814/60‑1 (MQ=255)
aaTCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa < 1:2991261/71‑1 (MQ=255)
aaTCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa < 1:770190/71‑1 (MQ=255)
aaTCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa < 1:787726/71‑1 (MQ=255)
tGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGt > 1:253814/1‑70 (MQ=255)
cTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:3681573/45‑1 (MQ=255)
cTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:604216/45‑1 (MQ=255)
cTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:1530454/45‑1 (MQ=255)
cTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:115555/45‑1 (MQ=255)
cTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:2503066/45‑1 (MQ=255)
cTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:2215156/45‑1 (MQ=255)
cTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:1487847/45‑1 (MQ=255)
cTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAt > 1:1262668/1‑71 (MQ=255)
cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAAATGTTCATGCCGAAACTAACAAACTGGTGAtt > 1:2528975/1‑70 (MQ=255)
gCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGAtt < 1:2892397/69‑1 (MQ=255)
tATTCTGCTGCCTTGCGCACTGGCATTGAGCACATCTGtt < 1:2274417/40‑1 (MQ=255)
tATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:1431751/40‑1 (MQ=255)
tATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:2485703/40‑1 (MQ=255)
tATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:217521/40‑1 (MQ=255)
tATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt < 1:2062981/40‑1 (MQ=255)
|
TAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATT > W3110S.gb/1657497‑1657626
|
| 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
