Table 2.

Single nucleotide polymorphisms and Indels among 9311, PA64s, and Nipponbare.

Gene name	Genes on chromosomea			Regulation region
	9311	PA64s	SNP no.b	SNP ratec	Indel no.d	Indel lengthe
OsNCED1	Chr02_3173	Chr02_4135	43|33|10	0.0141|0.0108|0.0033	12|7|6	116|96|20
OsNCED2	Chr12_1047	Chr12_0855	31|139|158	0.0102|0.0425|0.0478	8|8|16	96|540|614
OsNCED3	Chr03_3073	Chr03_2198	NA|NA|NA	NA|NA|NA	NA|NA|NA	NA|NA|NA
OsNCED4	Chr07_0366	Chr07_0350	100|174|228	0.033|0.0577|0.0757	3|16|9	60|30|22
OsNCED5	Chr12_2021	Chr12_1628	53|125|125	0.0173|0.0399|0.0406	9|10|12	116|264|164
OsCYP707A5	Chr02_3170	Chr02_4132	7|17|11	0.0023|0.0054|0.0035	3|3|2	2|262|260
OsCYP707A6	Chr08_2087	Chr08_1729	37|38|3	0.012|0.012|0.001	16|13|7	32|58|56
OsCYP707A7	Chr09_1329	Chr09_1219	262|262|2	0.084|0.0845|0.0007	25|25|0	204|204|0
OsGA20ox1	Chr03_4546	Chr03_3632	9|10|1	0.003|0.0033|0.0003	6|4|3	80|36|44
OsGA20ox2	Chr01_4645	Chr01_4410	34|NA|NA	0.011|NA|NA	7|NA|NA	188|NA|NA
OsGA20ox3	Chr12_1260	Chr12_1026	0|0|0	0|0|0	0|0|2	0|0|2
OsGA20ox4	Chr05_1936	Chr05_1801	45|45|0	0.0147|0.0147|0	9|9|0	102|102|0
OsGA3ox1	Chr05_0563	Chr05_0539	28|28|0	0.009|0.009|0	18|18|0	242|242|0
OsGA3ox2	Chr01_0611	Chr01_0665	40|40|0	0.0133|0.0133|0	6|6|0	12|12|0
OsGA2ox1	Chr05_0449	Chr05_0429	5|NA|NA	0.0016|NA|NA	6|NA|NA	10|NA|NA
OsGA2ox2	Chr01_0837	Chr01_0926	19|14|7	0.0063|0.0047|0.0023	11|6|8	28|18|12
OsGA2ox3	Chr01_3778	Chr01_3512	36|39|3	0.0119|0.0129|0.001	7|7|0	42|42|0
OsGA2ox4	Chr05_2528	Chr05_2378	370|18|348	0.117|0.0059|0.1103	69|10|67	306|76|306
OsGA2ox5	Chr05_2857	Chr05_2689	36|33|7	0.012|0.011|0.0023	6|5|4	10|6|8
OsGPCR	Chr10_1648	Chr10_1340	NA|25|NA	0.5375|0.0079|0.5209	80|11|95	184|340|228
OsGID1	Chr05_1857	Chr05_1721	NA|NA|NA	NA|NA|NA	NA|NA|NA	NA|NA|NA