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 |
1,712,949 |
G→A |
40.0% |
A828V (GCC→GTC) |
yphG ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,712,949 | 0 | G | A | 40.0%
| 24.7
/ 34.3
| 56 | A828V (GCC→GTC) | yphG | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (9/24); new base A (6/16); total (16/40) |
| 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 |
GTCGTCGCGTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCT > minE/1712885‑1713012
|
gtcgtcGCGTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTcc > 1:669367/1‑69 (MQ=255)
gtcgtcGCGTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTcc > 1:320036/1‑69 (MQ=255)
gtcgtcGCGTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTcc > 1:2299692/1‑69 (MQ=255)
gtcgtcGCGTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTc < 1:1708336/68‑1 (MQ=255)
tcgtcgCGTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCa > 1:2149060/1‑69 (MQ=255)
tcgtcgCGTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCa > 1:146579/1‑69 (MQ=255)
tcgtcgCGTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCa > 1:1471480/1‑69 (MQ=255)
cgcgTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCactta < 1:1115313/69‑1 (MQ=255)
cgcgTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCactta < 1:1969889/69‑1 (MQ=255)
cgcgTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCactta < 1:1448495/69‑1 (MQ=255)
aTTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGCCACCGCTTAACTTATCCAGCaaa > 1:1892127/1‑69 (MQ=255)
aTTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGACACCGCTTAAGTTATCCAGCaaa > 1:2523390/1‑69 (MQ=255)
aTTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGACACCGCTTAACTTATCCAGCaaa > 1:2774016/1‑69 (MQ=255)
aTTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGACACCGCTTAACTTATCCAGCaaa > 1:2703612/1‑69 (MQ=255)
aTTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGACACCGCTTAACTTATCCAGCaaa > 1:2847465/1‑69 (MQ=255)
aTTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGACACCGCTTAACTTATCCAGCaaa > 1:1718069/1‑69 (MQ=255)
aTTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGACACCGCTTAACTTATCCAGCaaa > 1:793490/1‑69 (MQ=255)
aGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCg < 1:2553207/68‑1 (MQ=255)
aGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCg < 1:3192503/68‑1 (MQ=255)
aGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCg < 1:2295028/68‑1 (MQ=255)
aGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCg < 1:803095/68‑1 (MQ=255)
aGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCg < 1:963194/68‑1 (MQ=255)
aGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCg < 1:115100/68‑1 (MQ=255)
aGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCg < 1:174007/68‑1 (MQ=255)
gATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCg < 1:1665831/67‑1 (MQ=255)
ttattTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCGtt > 1:518270/1‑67 (MQ=255)
ttattTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCGtt > 1:2901967/1‑67 (MQ=255)
ttattTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCGTTc > 1:3215107/1‑68 (MQ=255)
cAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCa < 1:946221/68‑1 (MQ=255)
cGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCa < 1:115434/63‑1 (MQ=255)
cGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCa < 1:1402191/63‑1 (MQ=255)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:10219/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:1773934/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:65507/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:46697/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:1403923/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:3137012/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:3025847/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:1504680/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:144351/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:1566458/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:2605768/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:2504299/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:2461721/43‑1 (MQ=37)
tcCGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:1747697/43‑1 (MQ=37)
tcCGGGGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:2254755/43‑1 (MQ=25)
ccGGTGTGACACCGCTTAACTTATCCAGCAAATCCCGTTCGa < 1:2943809/42‑1 (MQ=37)
gtgtGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCt < 1:1990357/69‑1 (MQ=255)
gtgtGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCt < 1:1994317/69‑1 (MQ=255)
gtgtGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCt < 1:900110/69‑1 (MQ=255)
gtgtGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCt < 1:2197512/69‑1 (MQ=255)
gtgtGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCt < 1:1362976/69‑1 (MQ=255)
gtgtGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCt < 1:1719918/69‑1 (MQ=255)
gtgtGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCt < 1:2321122/69‑1 (MQ=255)
gtgtGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCt < 1:1650561/69‑1 (MQ=255)
gtgtGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCt < 1:2914256/69‑1 (MQ=255)
|
GTCGTCGCGTTTCAGCGCAATTTCCAGATTATTTTCCAGACGCGCCAGTCGTTTCTCCGGTGTGGCTCCACTTAACTTATCCAGCAAATCCCGTTCGAAAAGCAGACGTGCATCCTGCGGCGCAAGCT > minE/1712885‑1713012
|
| 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
