|
Chrom.
|
Gene
|
mRNA
|
5’-UTR
|
CDS
|
Intron
|
3’-UTR
|
Intergenic
|
Total
|
Syn
|
Non-syn
|
Total
|
Non-syn/Syn
|
|---|
|
Chr1
|
634,912
|
630,396
|
25,880
|
291,817
|
286,601
|
26,098
|
1,252,989
|
1,887,901
|
118,095
|
173,722
|
291,817
|
1.471
|
|
Chr2
|
528,417
|
524,172
|
20,087
|
243,967
|
238,738
|
21,380
|
1,013,475
|
1,541,892
|
97,306
|
146,661
|
243,967
|
1.507
|
|
Chr3
|
490,402
|
487,611
|
19,899
|
223,196
|
224,129
|
20,387
|
962,304
|
1,452,706
|
88,477
|
134,719
|
223,196
|
1.523
|
|
Chr4
|
730,310
|
727,473
|
19,018
|
388,220
|
301,071
|
19,164
|
1,176,274
|
1,906,584
|
160,101
|
228,115
|
388,220
|
1.425
|
|
Chr5
|
489,370
|
485,848
|
13,623
|
257,327
|
200,307
|
14,591
|
867,799
|
1,357,169
|
103,723
|
153,604
|
257,327
|
1.481
|
|
Chr6
|
560,506
|
557,361
|
16,943
|
280,933
|
242,635
|
16,850
|
1,023,473
|
1,583,979
|
114,625
|
166,308
|
280,933
|
1.451
|
|
Chr7
|
548,266
|
546,569
|
16,210
|
280,994
|
231,797
|
17,568
|
973,670
|
1,521,936
|
115,332
|
165,662
|
280,994
|
1.436
|
|
Chr8
|
582,068
|
580,181
|
16,396
|
302,785
|
244,991
|
16,009
|
998,651
|
1,580,719
|
124,025
|
178,759
|
302,785
|
1.441
|
|
Chr9
|
436,037
|
434,440
|
10,692
|
222,916
|
190,025
|
10,807
|
763,771
|
1,199,808
|
90,299
|
132,617
|
222,916
|
1.469
|
|
Chr10
|
476,710
|
473,603
|
11,735
|
258,013
|
192,214
|
11,641
|
806,940
|
1,283,650
|
109,451
|
148,561
|
258,013
|
1.357
|
|
Chr11
|
684,803
|
681,891
|
16,642
|
354,874
|
291,049
|
19,326
|
1,148,735
|
1,833,538
|
140,772
|
214,101
|
354,874
|
1.521
|
|
Chr12
|
607,336
|
603,783
|
16,549
|
319,401
|
251,103
|
16,730
|
1,055,044
|
1,662,380
|
129,296
|
190,105
|
319,401
|
1.470
|
|
ChrUn
|
19,706
|
19,706
|
0
|
12,615
|
7,091
|
0
|
26,669
|
46,375
|
5,819
|
6,796
|
12,615
|
1.168
|
|
ChrSy
|
11,463
|
11,463
|
0
|
7,913
|
3,550
|
0
|
15,043
|
26,506
|
3,846
|
4,067
|
7,913
|
1.057
|
|
Total
|
6,800,306
|
6,764,497
|
203,674
|
3,444,971
|
2,905,301
|
210,551
|
12,084,837
|
18,885,143
|
1,401,167
|
2,043,797
|
3,444,971
|
1.459
|
- The MSU V7.0 rice gene annotation for 55,986 genes and 66,338 mRNA [13] as a raw gff3 file type was downloaded from the Rice Genome Project Annotation ftp site [19]. Prior to categorization of SNP types, the raw gff3 file was processed 1) to remove all but the primary mRNA transcript and 2) to select the gene models with the highest support in cases where there are overlapping gene models. Hence, SNP characteristics are reported here for 55,107 of the 55,986 gene models. Characteristics of SNPs in pseudogenes or where the reference base is N (unknown or missing) are not reported. Syn = synonymous; Non-syn = non-synonymous.
