General statistics for JSNP database

Total number of JSNP variations available 197195
Total number of variations in IMS-JST SNP discover project 189526
Total number of variations in other laboratory's discover project 7669

Total number of the relations among JSNP variations 1824
Total number of JSNP SNPs with allele frequencies 84651
Note: Relations means homology among existing JSNP and newly submitted variations (from other laboratory's discover project).
We screened all new variations against existing JSNP entries by blast homology between the flanking sequences.

1. The statistics of mapping result,JSNP variations to the NCBI human genome sequence assembly (37 version3)

Summary
Unmapped variations 9429
Single hit 185834
Multiple hits sub total 1932
Total 197195
  Details of Multi hits
2 hits 1528
3 hits 280
4 hits 48
5 hits 36
6 hits 16
7 hits 8
8 hits 1
10 hits 1
11 hits 1
12 hits 1
15 hits 3
16 hits 2
19 hits 1
21 hits 1
22 hits 3
23 hits 2

2. The number of Ensembl transcript (v65) having at least one JSNP variations

Ensembl transcript in NCBI genome assembly 88774
having at least one JSNP variation
5'-UTR/ 3'-UTR/ CDS/ intron of Ensembl transcript 62182
2.5Kbp upstream of 5'-UTR/
5'-UTR/ 2.5Kbp downstream of 3'-UTR/ 3'-UTR/ CDS/ intron of Ensembl transcript		 71529

3. The number of RefSeq XM/NM (37 version3) having at least one JSNP variations

RefSeq XM/NM entries in NCBI human genome assembly 32105
having at least one JSNP variation
5'-UTR/ 3'-UTR/ CDS/ intron of RefSeq XM/NM 25297
2.5Kbp upstream of 5'-UTR/
5'-UTR/ 2.5Kbp downstream of 3'-UTR/ 3'-UTR/ CDS/ intron of RefSeq XM/NM		 27226

4. The number of JSNP location, annotated with Ensembl transcript (v65)

Total Single hit Multi hits
Total SNP Insertion/ Deletion Total SNP Insertion/ Deletion Total SNP Insertion/ Deletion
CDS 14964 14745 265 14459 14257 202 505 488 17
5'-UTR 2278 2108 180 2228 2061 167 50 47 3
3'-UTR 8438 7396 1043 8334 7308 1026 104 88 16
Promoter 14559 13150 1436 14124 12759 1365 435 391 44
Intron 126613 115278 11436 125029 113929 11100 1584 1349 235
3'-flanking 5962 5271 696 5800 5123 677 162 148 14
Other 17710 16317 1487 15860 14634 1226 1850 1683 167
total 190524 174265 16543 185834 170071 15763 4690 4194 496
Note: Promoter ... 2.5Kb interval of 5'upstream of RefSeq XM/NM
3'-flanking ... 2.5Kb interval of 5'downstream of RefSeq XM/NM
Note: The mapped JSNP locations may have several gene structures among different Ensembl transcript, but gene structure is put in the order of priority; 1)CDS, 2)5'-UTR, 3)3'-UTR, 4)Promoter, 5)Intron, 6)3'-flanking and 7)Other.

5. The number of JSNP location, annotated with RefSeq XM/NM (37 version3)

Total Single hit Multi hits
Total SNP Insertion/ Deletion Total SNP Insertion/ Deletion Total SNP Insertion/ Deletion
CDS 15601 15322 291 15077 14820 257 524 502 22
5'-UTR 2376 2183 194 2336 2149 187 40 34 6
3'-UTR 12848 11294 1556 12671 11146 1525 177 148 29
Promoter 21097 19107 2009 20682 18740 1942 415 367 48
Intron 110759 100830 9958 109331 99614 9717 1428 1216 212
3'-flanking 3625 3241 387 3512 3132 380 113 109 4
total 166306 151977 14395 163609 149601 14008 2697 2376 321
Note: Promoter ... 2.5Kb interval of 5'upstream of RefSeq XM/NM
3'-flanking ... 2.5Kb interval of 5'downstream of RefSeq XM/NM
Note: The mapped JSNP locations may have several gene structures among different RefSeq XM/NM, but gene structure is put in the order of priority; 1)CDS, 2)5'-UTR, 3)3'-UTR, 4)Promoter, 5)Intron, 6)3'-flanking and 7)Other.

6. The number of JSNP locations mapped to chromosomes

Single hit Multiple hits in a chromosome Multiple hits in genome
Total SNP Insertion/
Deletion		 Total SNP Insertion/
Deletion		 Total SNP Insertion/
Deletion
Chr.1 18522 16934 1588 361 332 29 46 37 9
Chr.2 15517 14087 1430 203 154 49 16 13 3
Chr.3 11221 10183 1038 42 30 12 10 10
Chr.4 7796 6993 803 118 106 12 27 24 3
Chr.5 10081 9125 956 178 162 16 4 4
Chr.6 14616 13299 1317 167 145 22 25 24 1
Chr.7 14154 12965 1189 350 310 40 25 23 2
Chr.8 5324 4863 461 218 212 6 9 8 1
Chr.9 6575 6039 536 146 119 27 5 5
Chr.10 6994 6423 571 295 261 34 3 3
Chr.11 7825 7215 610 55 46 9 12 12
Chr.12 8775 7995 780 67 59 8 17 16 1
Chr.13 3496 3159 337 30 24 6 2 1 1
Chr.14 6812 6270 542 94 72 22 27 26 1
Chr.15 5038 4622 416 336 312 24 2 2
Chr.16 6083 5676 407 303 285 18 15 15
Chr.17 7041 6456 585 244 208 36 17 16 1
Chr.18 2743 2487 256 22 18 4 2 2
Chr.19 8279 7704 575 268 256 12 3 3
Chr.20 5712 5280 432 10 4 6 2 2
Chr.21 4073 3762 311 6 6 7 6 1
Chr.22 5649 5331 318 251 227 24 52 48 4
Chr.X 3483 3179 304 294 276 18 78 70 8
Chr.Y 25 24 1 148 136 12 78 70 8
Multiple hits
variations		 1932 1711 221
Unmapped
variations		 9429 8302 1127
Total 197195

7. The number of the sequenced bases annotated with RefSeq XM/NM (37 version3)

sequenced not sequenced repeat total
CDS
 		 17772321
(52%)		 15799204
(46%)		 187357
(0%)		 33758882
 
5'-UTR
 		 1743414
(45%)		 1863489
(49%)		 183443
(4%)		 3790346
 
3'-UTR
 		 6525457
(36%)		 9773212
(54%)		 1544360
(8%)		 17843029
 
Promoter
 		 10755040
(21%)		 27983387
(55%)		 11904133
(23%)		 50642560
 
Intron
 		 93707225
(8%)		 652989170
(61%)		 319888041
(29%)		 1066584436
 
3'-flanking
 		 4622030
(12%)		 23339742
(62%)		 9189009
(24%)		 37150781
 
Other
 		 13940192
(0%)		 761696823
(40%)		 1109390363
(58%)		 1885027378
 
Total
 		 149065679
(4%)		 1493445027
(48%)		 1452286706
(46%)		 3094797412
 
Note: Promoter ... 2.5Kb interval of 5'upstream of RefSeq XM/NM
3'-flanking ... 2.5Kb interval of 5'downstream of RefSeq XM/NM
Note: The mapped JSNP locations may have several gene structures among different RefSeq XM/NM, but gene structure is put in the order of priority; 1)CDS, 2)5'-UTR, 3)3'-UTR, 4)Promoter, 5)Intron, 6)3'-flanking and 7)Other.

8. The number of the sequenced bases annotated with RefSeq XM/NM (37 version3),
by chromosome

by chromosome

9. The statistics of SNPs according to codon position

Number of SNPs Number of SNPs
with allele frequency data
First base of codon 3229 1798
Second base of codon 2828 1514
Third base of codon 7666 4782
Total 13723 8094

10. The statistics of SNPs according to amino acid substitution, using NCBI human genome assembly (37 version3) and BLOSUM62

Number of SNPs Number of SNPs
with allele frequency data
Total 13723 8094
Synonymous 7594 4770
Non synonymous 6129 3324
Nonsense 61 18
Missense 6068 3306
Conservative 3648 2052
Non conservative 2420 1254

11. Amino acid substitution of SNPs, using NCBI human genome assembly (37 version3) and BLOSUM62

C 103
S 65 760
T 0 101 726
P 0 185 48 838
A 0 109 322 88 834
G 20 171 0 0 77 445
N 0 181 29 0 0 0 309
D 0 0 0 0 34 91 108 378
E 0 0 0 0 42 90 0 125 236
Q 0 0 0 29 0 0 0 0 79 186
H 0 0 0 24 0 0 18 32 0 96 251
R 141 71 24 59 0 173 0 0 0 333 251 335
K 0 0 24 0 0 0 48 0 171 41 0 131 179
M 0 0 159 0 0 0 0 0 0 0 0 8 2 0
I 0 22 164 0 0 0 9 0 0 0 0 8 5 62 253
L 0 77 0 234 0 0 0 0 0 16 16 47 0 38 26 799
V 0 0 0 0 242 46 0 13 12 0 0 0 0 201 362 132 371
F 13 44 0 0 0 0 0 0 0 0 0 0 0 0 10 116 16 173
Y 69 22 0 0 0 0 11 12 0 0 57 0 0 0 0 0 0 11 260
W 16 3 0 0 0 10 0 0 0 0 0 123 0 0 0 3 0 0 0 0
X 2 4 0 0 0 0 0 0 4 19 0 18 0 0 0 2 0 0 6 6 2
C S T P A G N D E Q H R K M I L V F Y W X
Total8094
Synonymous4770
Non synonymous3324
  Nonsense18
  Missense3306
    Conservative2052
    Non conservative1254
Note: Blue background means conservative change.
Note: X means stop codon.
Note: Major -> Minor is correspond to vertical index -> horizontal index.

12. Amino acid substitution of SNPs with allele frequency data ,using NCBI human genome assembly (37 version3) and BLOSUM62

C 65 16 0 0 0 8 0 0 0 0 0 49 0 0 0 0 0 5 16 5 0
S 19 457 31 66 31 69 64 0 0 0 0 15 0 0 3 9 0 7 4 1 0
T 0 28 467 23 100 0 5 0 0 0 0 5 7 32 46 0 0 0 0 0 0
P 0 24 6 500 28 0 0 0 0 9 1 20 0 0 0 34 0 0 0 0 0
A 0 19 62 22 508 20 0 4 15 0 0 0 0 0 0 0 50 0 0 0 0
G 4 33 0 0 21 257 0 21 15 0 0 27 0 0 0 0 8 0 0 3 0
N 0 48 4 0 0 0 194 41 0 0 2 0 17 0 1 0 0 0 3 0 0
D 0 0 0 0 12 26 17 268 37 0 6 0 0 0 0 0 3 0 4 0 0
E 0 0 0 0 11 24 0 27 154 26 0 0 41 0 0 0 4 0 0 0 1
Q 0 0 0 11 0 0 0 0 19 125 25 125 11 0 0 4 0 0 0 0 1
H 0 0 0 14 0 0 10 7 0 34 167 97 0 0 0 4 0 0 10 0 0
R 24 17 5 13 0 57 0 0 0 52 44 195 56 4 2 10 0 0 0 18 0
K 0 0 5 0 0 0 11 0 61 16 0 33 110 1 0 0 0 0 0 0 0
M 0 0 65 0 0 0 0 0 0 0 0 0 1 0 21 13 81 0 0 0 0
I 0 7 33 0 0 0 0 0 0 0 0 4 3 21 175 8 111 1 0 0 0
L 0 28 0 89 0 0 0 0 0 5 2 9 0 10 6 515 53 20 0 0 0
V 0 0 0 0 71 21 0 2 2 0 0 0 0 39 102 26 225 2 0 0 0
F 2 16 0 0 0 0 0 0 0 0 0 0 0 0 1 42 5 116 3 0 0
Y 10 7 0 0 0 0 4 4 0 0 23 0 0 0 0 0 0 3 182 0 1
W 7 1 0 0 0 0 0 0 0 0 0 57 0 0 0 1 0 0 0 0 0
X 0 1 0 0 0 0 0 0 1 6 0 2 0 0 0 0 0 0 1 4 2
C S T P A G N D E Q H R K M I L V F Y W X
Total13723
Synonymous7594
Non synonymous6129
  Nonsense61
  Missense6068
    Conservative3648
    Non conservative2420
Note: Blue background means conservative change.
Note: X means stop codon.