Finding and extending ancient simple sequence repeat-derived regions in the human genome

Table 1 SSR-clouds recovery of Tandem Repeats Finder (TRF) loci

		Highest Cloud Stringency of Locus						FDR ≤ %5
		Perfect Repeats		Mid-stringency		Low Stringency		FDR ≤ %5
		Loci	bp	Loci	bp	Loci	bp	Loci	bp
Poly-A	SSR-Clouds TRF Intersection	453,128	11,518,426	615,893	16,085,955	665,794	17,373,114	660,469	17,272,038
	Total SSR-Cloud Recovery of TRF	67.73%	62.37%	92.06%	87.10%	99.52%	94.07%	98.72%	93.52%
	Novel Clouds	244,269	13,490,320	889,630	36,272,378	2,282,559	65,260,452	1,552,401	53,363,205
(AC_)n	SSR-Clouds TRF Intersection	120,498	4,813,795	143,941	5,989,636	148,027	6,301,466	148,027	6,301,466
	Total SSR-Cloud Recovery of TRF	81.09%	65.02%	96.86%	80.90%	99.61%	85.11%	99.61%	85.11%
	Novel Clouds	28,365	3,444,295	724,496	25,393,739	1,621,096	44,746,021	1,621,096	44,746,021
All Motifs	SSR-Clouds TRF Intersection	1,741,873	59,642,996	1,965,320	67,616,136	2,119,405	71,906,834	1,946,410	68,221,956
	Total SSR-Cloud Recovery of TRF	78.73%	67.40%	88.83%	76.41%	95.80%	81.26%	87.98%	77.10%
	Novel Clouds	2,046,914	58,749,285	2,690,429	75,993,192	6,702,981	149,673,223	2,008,354	70,732,930

SSR-clouds loci with a merge distance of 5 bp were divided into 3 nested sets based on the most stringent oligo used to annotate each locus and compared to TRF loci. Comparisons were also made for SSR-clouds loci with FDR ≤ 5%. Cells in the table report the number of loci that overlap TRF loci and the number of bp within overlapping loci. We also report the number of novel SSR-clouds loci and bp. Recovery percentages are reported relative to the total number of TRF loci in each comparison category (Poly-A: 669,020; (AC)_n: 148,607; All Motifs: 2,212,424) and total length in bp of the TRF loci (Poly-A: 18,468,468; (AC)_n: 7,403,867; All Motifs: 88,485,889)

ISSN: 1759-8753