2_5 Female and Male X Chromosome Informative SNPs (Version 2) |
shunping / Version 10 |
This is the second version of Informative SNPs. It can be downloaded from here.
Version 1 vs. Version 2:
First, the main difference between these two version is the criterion for pruning SNPs.
- In version 1, we masked SNPs where less than 75% of samples have pileup height >=50.
- In version 2, we masked SNPs where less than 1 sample has pileup height >= 50.
Second, we have added a new flag in the data set showing whether each SNP is good in their maternal and/or paternal inbred strains.
Third, We run the same procedure on male F1s.
Summary:
FG/GF Female
|
Total |
eSNPs |
intergenic |
FG |
3132 |
2651 |
481 |
GF |
3273 |
2706 |
567 |
Intersection |
2981 |
2544 |
437
|
|
FG/GF Male
|
Total |
eSNPs |
intergenic |
FG |
3292 |
2704 |
588 |
GF |
2712 |
2287 |
425 |
Intersection |
2499 |
2238 |
261 |
|
FH/HF Female
|
Total |
eSNPs |
intergenic |
FH |
2578 |
2095 |
483 |
HF |
2393 |
1937 |
456 |
Intersection |
2310 |
1878 |
432 |
|
FH/HF Male
|
Total |
eSNPs |
intergenic |
FH |
2483 |
2034 |
449 |
HF |
2522 |
2135 |
387 |
Intersection |
2202 |
1904 |
298 |
|
GH/HG Female
|
Total |
eSNPs |
intergenic |
GH |
4096 |
2816 |
1280 |
HG |
4370 |
2910 |
1460 |
Intersection |
3887 |
2714 |
1173 |
|
GH/HG Male
|
Total |
eSNPs |
intergenic |
GH |
2533 |
2096 |
437 |
HG |
2882 |
2429 |
453 |
Intersection |
2265 |
2027 |
238 |
|
Detailed Procedure:
Please refer to Version 1 and the difference.
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