Summary stats for SNP density, 1mb windows
(2,754 windows, no unbridged gaps)
Venter
Watson
Ceu
Yri
Chb
Jpt
Sum
Mean
Stdev
0%
25%
50%
75%
100%
3248704
1179
420
17
936
1182
1415
6606
1989392
722
245
0
587
740
875
2172
2670808
969
343
0
768
976
1178
3222
2938231
1066
364
0
847
1073
1293
3307
2520952
915
331
0
717
920
1114
3146
2489482
903
328
0
710
909
1104
3102
*using base coverage, feature
coverage never finishes
** Sums reflect regions smaller
than window size being thrown out
SNP density 100kb windows (28,442)
Venter
Watson
Ceu
Yri
Chb
Jpt
dbSNP
126
Sum
Mean
Stdev
0%
25%
50%
75%
100%
3347391
117
69
0
71
113
156
1851
2052667
72
41
0
45
71
97
1107
2725973
95
47
0
63
93
125
557
2998514
105
50
0
71
102
136
557
2573242
90
46
0
58
87
119
622
2541151
89
46
0
57
86
117
574
12266167
430
259
20
303
386
496
12479
dbSNP 126 has 12million SNPs, including randoms , etc.
The region with the most SNPs is chr16 44943302-45043302
Regions with no SNPs (100kb)
• Watson and Venter have 121 regions in
common (292 & 162)
• All HapMap has 444 in common (469-487)
• They all have 111 in common
– dbSNP has entries in these regions
– Ensembl has a few Watson SNPs and many Venter
SNPs (only 2 in chrY remained 0) here
Genome Graphs import uses a
10kb window for computing depth
and coverage. For these graphs
depth was chosen and connections
were drawn between items up to
1mb away. Ceu was done with
both 1mb connections and 10kb
connections and there wasn’t a
noticeable difference.
Graph A
Watson
Venter
Ceu
Watson
Graph B
ceu
yri
chb
jpt
ceu
yri
chb
jpt
yri
Venter
R
.547
.511
.553
.554
.463
.424
.470
.471
.942
.539
R-Squared
.299
.261
.306
.307
.214
.180
.221
.221
.888
.290
Allele comparisons
Watson
Venter
Exact match 1 or more
Exact match 1 or more
Ceu
38.9%
49.2%
21.2%
37.5%
Chb
37.0%
48.3%
21.3%
36.6%
Jpt
36.5%
48.0%
21.2%
36.4%
Yri
38.0%
47.3%
18.3%
35.9%
Percent = (matches/total SNPs)*100
Total SNPs is Watson or Venter
1 or more includes the exact matches
Coding SNPs (RefSeq Genes)
• Watson
– 857 substitutions
• 779 in dbSNP 128
• 706 heterozygous
• Venter
– 13 frameshifts
• 1 in dbSNP 128
• 13 heterozygous
– 1109 substitutions
• 1003 in dbSNP 128
• 648 heterozygous
Comparing Venter’s deletion to
alignments
• 96,181 deletions
• Extracted maf for +- 2bps of deletions
• Found no deletions in other species at the
same locations
• Found from 0 to 27 species with alignments
– Mean 2 per deletion, median 1, max 27
– chr9 36092117
36092118
A/-
The max region
The gene
OMIM
Watson homozygous? SNPs
• Only 1 allele found, not guaranteed homozygous
• Found 382024 SNPs
• matching species: min 0, max 27 (2 SNPs), ave 3,
median 2
– 18,935 with 10 or more species
• aligned but not matching: min 0, max 27 (2
SNPs), ave 3, median 2
– 25,663 with 10 or more species
Venter Homozygous? SNPs
•
•
•
•
Only 1 allele found, not guaranteed homozygous
1,450,836 SNPs
matching species: min 0, max 27 ,ave 3, median 2
aligned but not matching: min 0, max 27, ave 3,
median 2