Flexible and scalable genotyping-by-sequencing strategies for population studies

BMC Genomics

Table 3 Genic fractions of total and covered predicted sites

	MlyI	AluI	RsaI	DraI	EcoRV	StuI	HaeIII	HincII
				Maize
Fraction total predicted genic sites	0.0668	0.0868	0.0957	0.0921	0.1021	0.0921	0.0836	0.1040
Fraction predicted genic sites 100-1000 bp	0.0621	0.0900	0.0982	0.0766	0.0820	0.0542	0.0823	0.0967
Fraction predicted genic sites 100-400 bp	0.0543	0.0908	0.1011	0.0624	0.0940	0.0428	0.0804	0.0953
Fraction genic sites 100-200 bp	0.0538	0.0900	0.1068	0.0560	0.0780	0.0495	0.0804	0.0865
Fraction total covered sites genic*	0.0657	0.1368	0.1531	0.0768	0.1067	0.0669	0.1007	0.2031
Fraction covered sites genic 100-1000 bp*	0.0660	0.1321	0.1488	0.0757	0.1050	0.0646	0.0967	0.1993
Fraction covered sites genic 100-400 bp*	0.0638	0.1317	0.1484	0.0742	0.1093	0.0664	0.0964	0.1958
Fraction covered sites genic 100-200 bp*	0.0630	0.1321	0.1503	0.0661	0.0928	0.0763	0.0961	0.1737
				Rice
Fraction total predicted genic sites	0.3102	0.3342	0.3070	0.2196	0.3917	0.3794	0.2756	0.3561
Fraction predicted genic sites 100-1000 bp	0.2793	0.3367	0.3261	0.1721	0.3124	0.2261	0.2977	0.3021
Fraction predicted genic sites 100-400 bp	0.2471	0.3442	0.3112	0.1439	0.2790	0.2084	0.2910	0.3021
Fraction genic sites 100-200 bp	0.2244	0.3468	0.3041	0.1328	0.3016	0.2417	0.2929	0.2867
Fraction total covered sites genic*	0.2588	0.3871	0.3487	0.1619	0.3321	0.3455	0.3240	0.4336
Fraction covered sites genic 100-1000 bp*	0.2625	0.3837	0.3502	0.1646	0.3334	0.3413	0.3222	0.4178
Fraction covered sites genic 100-400 bp*	0.2587	0.3796	0.3435	0.1504	0.2970	0.2958	0.3180	0.4178
Fraction covered sites genic 100-200 bp*	0.2423	0.3825	0.3366	0.1395	0.3158	0.3019	0.3241	0.4060

*A read alignment with MQ ≥20 is required for a site to be considered “covered”.

ISSN: 1471-2164