quality filtered and barcodes removed
MA1 - 2.4 million
MA2 - 23 k
MA3 - 2.8 million
MA4 - 3.1 million
MAX3 - 3.5 million
MAX2 - 4.7 million
MAX9 - 3.0 milion
MAX11 - 3.3 million
MA_All_qf - 8.4 million
MAX_All_qf - 14.5 million
MA denovo
MA SNP
Annotate consensus sequence = No
Annotate reference sequence = Yes
Create table = Yes
Genetic code translation = Standard
Maximum coverage = 1000
Maximum expected variations (ploidy) = 2
Maximum gap and mismatch count = 2
Minimum average quality = 15
Minimum central quality = 20
Minimum coverage = 10
Minimum paired coverage = 0
Minimum variant frequency (%) = 35.0
Required variant count threshold = 1
Sufficient variant count threshold = 5
Use advanced significance settings = Yes
Window length = 11
--
1372 SNPs
235776
1372/235776
1372/225952
MAX de novo
MAX=BARN
-
543 SNPs
107784 total bases (based on avg)
543/107784 = 0.005038 SNP / BP
| BARN |
MASH |
|
| 12.92134831 |
10.15567087 |
A/C |
| 27.71535581 |
28.68791698 |
A/G ** |
| 18.35205993 |
18.45811712 |
A/T |
| 7.116104869 |
5.633802817 |
C/G |
| 21.91011236 |
25.94514455 |
C/T ** |
| 11.98501873 |
11.11934766 |
G/T |
