SNP-markers in Allium species to facilitate introgression breeding in onion

BMC Plant Biology

Table 2 General statistics of the Illumina sequencing, assembly and number of reliable SNPs identified by QualitySNP in RF and the onion cultivars. RF and cultivars Bravo and Jumbo were analyzed in a seperate run (three genotypes in one lane). In the other run two cDNA samples of eight cultivars were multiplexed per lane

Genotype	Number of bases	Number of reads	Number of contigs	N50 ^a	Number of contigs with reliable SNPs ^b
RF	276,285,871	5,662,574	10,361	395	7990
Bravo	572,211,306	11,727,836	46,596	309	6920
Jumbo	346,687,223	7,108,700	36,897	276	6709
Babosa	2,682,844,988	25,031,165	99,010	602	38,520
California Red	1,965,911,851	18,940,653	81,574	623	31,471
Pukekohe Longkeeper	2,274,863,215	21,244,183	99,761	649	35,203
Rio Tinto	2,017,823,470	19,525,723	81,975	588	30,996
Rumba	2,054,901,823	18,835,004	103,178	561	38,735
Sapporo Yellow Globe	3,215,089,647	34,561,122	69,206	519	27,093
South Port White Globe	2,071,923,107	29,319,916	76,187	558	28,232

^a Average contig length in base pairs
^b A SNP is called a reliable SNP when every allele is present in at least 4 reads (Tang et al. [29])

ISSN: 1471-2229