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 |
1,576,228 |
T→C |
38.4% |
P272P (CCA→CCG) |
xapB ← |
xanthosine transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,576,228 | 0 | T | C | 38.4%
| 22.3
/ 32.2
| 52 | P272P (CCA→CCG) | xapB | xanthosine transporter |
| Reads supporting (aligned to +/- strand): ref base T (10/22); new base C (16/4); total (26/26) |
| Fisher's exact test for biased strand distribution p-value = 1.40e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.28e-01 |
GCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGAGGGA > minE/1576175‑1576288
|
gCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGtata < 1:2884267/69‑1 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGtata < 1:2690014/69‑1 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGtata < 1:2361101/69‑1 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTAAGtata < 1:441364/69‑1 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTAtc > 1:1036540/1‑59 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAg > 1:697944/1‑65 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:886772/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:665773/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:602423/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:532439/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:3161728/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:2556439/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:2536945/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:2299568/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:1435194/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:1615956/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:1311485/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:1143667/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACCGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:1182347/1‑68 (MQ=255)
gCCACCATACTCATCAGCATGACGGTTTTAATACAGAAACGCTTCAAAAAGAACGGTATCGTCAGaat > 1:1970310/1‑68 (MQ=255)
aCGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCtg > 1:3429267/1‑68 (MQ=255)
ttttAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGaaa < 1:1784649/69‑1 (MQ=255)
ttttAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGaaa < 1:235661/69‑1 (MQ=255)
ttttAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGaaa < 1:2650624/69‑1 (MQ=255)
ccAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAg > 1:2070951/1‑68 (MQ=255)
ccAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAg > 1:2691599/1‑68 (MQ=255)
aaacGCTTCAAAAAGAACGGTATCGTCAGAATGAAACCGACTTCAGCCATCTGTGAAACTGACAGTaaa < 1:1472237/66‑1 (MQ=255)
aaacGCTTCAAAAAGAACGGTATCGTCAGAATGAAACCGACTTCAGCCATCTGTGAAACTGACAGTaaa < 1:1320875/66‑1 (MQ=255)
aaacGCTTCAAAAAGAACGGTATCGTCAGAATGAAACCGACTTCAGCCATCTGTGAAACTGACAGTaaa < 1:3231138/66‑1 (MQ=255)
aaacGCTTCAAAAAGAACGGTATCGTCAGAATGAAACCGACTTCAGCCATCTGTGAAACTGACAGTaaa < 1:2510358/66‑1 (MQ=255)
cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaaa > 1:725445/1‑67 (MQ=255)
cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaaa > 1:89249/1‑67 (MQ=255)
cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaaa > 1:2524813/1‑67 (MQ=255)
cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaaa > 1:46413/1‑67 (MQ=255)
cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaa > 1:1144673/1‑66 (MQ=255)
cGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTaaa > 1:3302897/1‑66 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGaa < 1:2995924/53‑1 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg < 1:716408/69‑1 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg < 1:396346/69‑1 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg > 1:3105921/1‑69 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg < 1:647722/69‑1 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg < 1:682569/69‑1 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg < 1:1817558/69‑1 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATgg < 1:706163/69‑1 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCAGTGAAACTGACAGTAAAATgg < 1:1892274/69‑1 (MQ=255)
gCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTCCTGCCATCTGTGAAACTGACAGTAAAATgg < 1:172555/69‑1 (MQ=255)
tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTTAAACTGACAGTAAAATGGa < 1:1755786/68‑1 (MQ=255)
tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGa < 1:1110894/68‑1 (MQ=255)
tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGa < 1:387235/68‑1 (MQ=255)
tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGa < 1:2540205/68‑1 (MQ=255)
tttAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGa < 1:2131803/68‑1 (MQ=255)
aaaaGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGAGGGa < 1:2573645/68‑1 (MQ=255)
|
GCCACCATACTCATCAGCATGACGGTTTTAATGCCAAATCGCTTTAAAAAGAATGGGATAGTCAGTATAAAGCCCACTTCTGCCATCTGTGAAACTGACAGTAAAATGGAGGGA > minE/1576175‑1576288
|
| 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
