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 |
1,170,190 |
A→C |
30.4% |
P43P (CCA→CCC) |
gdhA → |
glutamate dehydrogenase, NADP‑specific |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,170,190 | 0 | A | C | 30.4%
| 46.0
/ 27.2
| 46 | P43P (CCA→CCC) | gdhA | glutamate dehydrogenase, NADP‑specific |
| Reads supporting (aligned to +/- strand): ref base A (9/23); new base C (7/7); total (16/30) |
| Fisher's exact test for biased strand distribution p-value = 1.89e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
AAACCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAGCGCGTGATCCAGTTTCGCGTGG > minE/1170123‑1170257
|
aaaCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaa < 1:2980359/69‑1 (MQ=255)
aaaCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaa < 1:2068559/69‑1 (MQ=255)
aaaCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaa < 1:692587/69‑1 (MQ=255)
aaaCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaa < 1:225572/69‑1 (MQ=255)
aaaCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaa < 1:1670588/69‑1 (MQ=255)
aaaCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaa < 1:2361845/69‑1 (MQ=255)
aaaCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaa < 1:3336105/69‑1 (MQ=255)
aaaCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaa < 1:1320768/69‑1 (MQ=255)
aCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaaaa < 1:1482901/69‑1 (MQ=255)
aCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaaaa < 1:978667/69‑1 (MQ=255)
aCCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaaaa < 1:2733917/69‑1 (MQ=255)
cgcgCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAatat > 1:810968/1‑64 (MQ=255)
cgcgCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATc > 1:348639/1‑65 (MQ=255)
cgcgCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATc > 1:1446009/1‑65 (MQ=255)
cgcgCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATc > 1:1484572/1‑65 (MQ=255)
cgcgCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATc > 1:2897282/1‑65 (MQ=255)
gcAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGAt < 1:2189208/69‑1 (MQ=255)
gcAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGAt < 1:1054553/69‑1 (MQ=255)
gcAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGAt < 1:1225099/69‑1 (MQ=255)
gcAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGAt < 1:932175/69‑1 (MQ=255)
gcAAGCCGTTCGTGAAGT‑ATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGAt < 1:3016157/68‑1 (MQ=255)
aaGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCaaaa < 1:2734049/56‑1 (MQ=255)
aaGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGt < 1:2046233/69‑1 (MQ=255)
cGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTAc > 1:1994602/1‑67 (MQ=255)
cGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTAc > 1:2648505/1‑67 (MQ=255)
cGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTAc > 1:141625/1‑67 (MQ=255)
cGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTAc > 1:2391728/1‑67 (MQ=255)
cGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTAc > 1:1788722/1‑67 (MQ=255)
cGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTAc > 1:525626/1‑67 (MQ=255)
cGTGAAGTAATGACCACACTCTGGCCTTTTCTCGAACAAAATCCCAAATATCGTCAGATGTCATTAc > 1:602639/1‑67 (MQ=255)
gTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTACTGGAGCg < 1:1741466/68‑1 (MQ=255)
gTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTACTGGAGCg < 1:2614394/68‑1 (MQ=255)
gTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTACTGGAGCg < 1:2828766/68‑1 (MQ=255)
gTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTACTGGAGCg < 1:2830381/68‑1 (MQ=255)
gTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTACTGGAGCg < 1:1202320/68‑1 (MQ=255)
tAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCCAAATATCGTCAGATGTCATTACTGGAGCg < 1:709445/67‑1 (MQ=255)
aTGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTg > 1:484075/1‑69 (MQ=255)
aTGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTg > 1:2243489/1‑69 (MQ=255)
cacaCTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGa < 1:3337504/69‑1 (MQ=255)
cacaCTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGa < 1:3127649/69‑1 (MQ=255)
cacaCTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGa < 1:298435/69‑1 (MQ=255)
cacaCTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGa < 1:110627/69‑1 (MQ=255)
cacaCTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGa < 1:276975/69‑1 (MQ=255)
cacaCTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGa < 1:1335055/69‑1 (MQ=255)
cacaCTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGa < 1:1546615/69‑1 (MQ=255)
cacTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAAc < 1:3249411/69‑1 (MQ=255)
cacTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAAc < 1:2438054/69‑1 (MQ=255)
cacTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAAc < 1:1619628/69‑1 (MQ=255)
cacTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAAc < 1:2129622/69‑1 (MQ=255)
acTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAAc < 1:2271957/68‑1 (MQ=255)
tctGGCCTTTTCTTTAACAAAATCCCAAATATCGTCAGATGTCATTACTGGAGCg < 1:1243296/55‑1 (MQ=255)
cTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAgcgc > 1:2422019/1‑68 (MQ=255)
cTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAgcgc > 1:1862881/1‑68 (MQ=255)
cAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAGCGCGTGATCCAGTTTCGCGTgg < 1:2076667/69‑1 (MQ=255)
cAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAGCGCGTGATCCAGTTTCGCGTgg < 1:3386739/69‑1 (MQ=255)
cAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAGCGCGTGATCCAGTTTCGCGTgg < 1:2509516/69‑1 (MQ=255)
cAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAGCGCGTGATCCAGTTTCGCGTgg < 1:2730289/69‑1 (MQ=255)
cAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAGCGCGTGATCCAGTTTCGCGTgg < 1:2776312/69‑1 (MQ=255)
aaaaTATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAGCGCGTGATCCAGTTTCGCGTgg < 1:468876/68‑1 (MQ=255)
|
AAACCGAGTTCGCGCAAGCCGTTCGTGAAGTAATGACCACACTCTGGCCTTTTCTTGAACAAAATCCAAAATATCGCCAGATGTCATTACTGGAGCGTCTGGTTGAACCGGAGCGCGTGATCCAGTTTCGCGTGG > minE/1170123‑1170257
|
| 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
