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 |
449,666 |
C→G |
70.2% |
L224L (CTG→CTC) |
kdpB ← |
potassium translocating ATPase, subunit B |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 449,666 | 0 | C | G | 70.2%
| 53.6
/ 28.6
| 47 | L224L (CTG→CTC) | kdpB | potassium translocating ATPase, subunit B |
| Reads supporting (aligned to +/- strand): ref base C (8/6); new base G (14/19); total (22/25) |
| Fisher's exact test for biased strand distribution p-value = 5.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.22e-01 |
GCCCCACGCGGAAAACGGCCACAGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGATCATCCG > minE/449600‑449734
|
gCCCCACGCGGAAAACGGCCACAGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATcagcag < 1:1007995/69‑1 (MQ=255)
ccccACGCGGAAAACGGCCACAGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGa < 1:2547125/69‑1 (MQ=255)
ccccACGCGGAAAACGGCCACAGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGa < 1:1102731/69‑1 (MQ=255)
ccccACGCGGAAAACGGCCACAGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGa < 1:1298357/69‑1 (MQ=255)
ccccACGCGGAAAACGGCCACAGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGa < 1:811990/69‑1 (MQ=255)
ccccACGCGGAAAACGGCCACAGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGa < 1:1746607/69‑1 (MQ=255)
ccccACGCGGAAAACGGCCACAGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGa < 1:172168/69‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCTGGGCAATCAGGAGAATGGTCAGGGCaa < 1:2318787/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCTATCGGGAGAATGGTCAGGGCaa < 1:3139180/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGTGAATGGTCAGGGCaa < 1:679922/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATTGTCAGGGCaa < 1:2398653/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:3318419/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:3355591/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:343744/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:3085592/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:3053887/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:3049561/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:2815173/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:667553/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:866347/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:94057/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:2797908/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:2298788/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:2123837/61‑1 (MQ=255)
aGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:2084928/61‑1 (MQ=255)
gCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCaa < 1:1648741/60‑1 (MQ=255)
gCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGtt > 1:1395145/1‑69 (MQ=255)
gCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGtt > 1:732219/1‑69 (MQ=255)
gCGGTTGCC‑‑TAAAAAGACGATAGTCAGGGCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGtttt > 1:2019668/1‑69 (MQ=39)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGc > 1:3047682/1‑49 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:2399559/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:1072813/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:879282/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:729424/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:1450056/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:612863/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:608906/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:596670/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:3186267/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:3139327/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:2107017/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGttttac > 1:2481871/1‑67 (MQ=255)
ttGCCAGTAAAAAGACGATAGTCAGGGCAATCAGGAGAATGGTCAGGGCAATCTCGTTCGGCGtttta > 1:582969/1‑67 (MQ=255)
gCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGt > 1:1709654/1‑69 (MQ=255)
gCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGt > 1:1103948/1‑69 (MQ=255)
aaaaaGACGATAGTCAGGGCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCtgt > 1:300640/1‑69 (MQ=255)
aaaaaGACGATAGTCAGGGCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCtgt > 1:772645/1‑69 (MQ=255)
gCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATcgcg > 1:1628645/1‑69 (MQ=255)
cagcagAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGatcat > 1:824757/1‑69 (MQ=255)
cagcagAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGatca > 1:2415478/1‑68 (MQ=255)
agcagAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGatcat > 1:2339932/1‑68 (MQ=255)
agcagAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGatcat > 1:2426889/1‑68 (MQ=255)
agcagAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGatcat > 1:1635464/1‑68 (MQ=255)
agcagAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACAATCGCGatcat > 1:835429/1‑68 (MQ=255)
cagAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGATCATCCg < 1:233227/69‑1 (MQ=255)
cagAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGATCATCCg < 1:1474878/69‑1 (MQ=255)
cagAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGATCATCCg < 1:412940/69‑1 (MQ=255)
|
GCCCCACGCGGAAAACGGCCACAGCGTGGCGGTTGCCAGTAAAAAGACGATAGTCAGGGCAATCAGCAGAATGGTCAGGGCAATTTCGTTCGGCGTTTTGCGTCGCTGTGCGCCTTCCACCATCGCGATCATCCG > minE/449600‑449734
|
| 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
