Table 1.

Country of origin, main traits interesting for breeders and sequencing statistics of 14 rice cultivars selected for genome sequencing in this study. Reads were mapped on the sequences of Nipponbare Os-Nipponbare-Reference-IRGSP-1.0. Number of reads, % of unique and duplicated reads and resulted mean coverages are reported. Number of total SNPs and number of total SNPs after filtering according to prediction significance, type and number of alleles and absence of repetitive sequences

Accession	Origin	Characteristic	Number of reads (× 103)	% unique reads	% duplicated reads	Mean coverage	SNPs vcf	SNPs filtered
Arroz da Terra	Portugal	Cold tolerance, earliness	80,492	78.9	0.14	39.9	465,830	117,170
Bahia	Spain	Parental, grain quality	78,446	78.2	0.20	38.3	341,451	84,321
Bomba	Spain	Landrace, grain quality	80,038	77.0	0.12	38.7	771,460	200,619
Gigante Vercelli	Italy	Blast resistance	69,031	78.1	0.09	33.8	592,763	111,351
Gleva	Spain	Grain type	78,505	78.6	0.12	38.7	564,829	141,363
Italica Livorno	Italy	Earliness, cold tolerance	72,919	79.7	0.20	36.3	404,125	91,806
Kalao	France	Blast resistance	75,052	76.9	0.13	36.4	1,025,081	253,553
L202	USA	Parental, grain type	78,854	77.1	0.14	38.3	989,104	269,476
Loto	Italy	earliness	71,612	78.2	0.19	35.1	527,474	106,014
LTH	China	Cold tolerance	77,667	77.7	0.10	37.8	573,944	149,950
M202	USA	Parental	69,364	79.1	0.14	34.5	669,310	124,931
Pavlovski	Russia	Earliness, grain type	66,962	80.1	0.16	33.6	396,196	69,894
Puntal	Spain	Grain quality	69,581	77.6	0.17	34.0	928,794	182,272
Senia	Spain	Grain type	81,376	79.7	0.16	40.6	358,900	100,783