Table 1.

Pairix performance for 2D querying of pairs files

Query region	Reads in region 1	Reads in regions 1 and 2	Time (s) Pairix	Time (s) Tabix	Tabix/Pairix
chr1:10 Mb–20 Mb|chr1:8 Mb–20 Mb	114 996	44 979	0.37	0.59	1.60
	184 351	66 471	0.57	0.89	1.57
chr1:10 Mb–100 Mb|chr1:8 Mb–20 Mb	1 052 486	44 979	0.60	4.34	7.22
	1 284 965	66 471	0.76	5.42	7.13
chr1:|chr1:8 Mb–20 Mb	2 133 783	44 979	0.90	8.92	9.91
	3 609 461	82 884	1.20	15.39	12.86
chr1:|chr1:8 Mb–200 Mb	2 133 783	1 307 808	2.41	10.02	4.16
	3 609 461	1 019 677	2.26	16.39	7.25
chr1:|chr1:	2 133 783	1 329 322	1.19	9.70	8.13
	3 609 461	1 473 651	1.96	16.15	8.23
chr13:10 Mb–20 Mb|chr13:8 Mb–20 Mb	114 707	53 103	0.37	0.56	1.51
	138 405	57 006	0.52	0.71	1.46

Note: Pairix performs efficient 2D querying of pairs files. The relative advantage of Pairix seems to increase with the number of reads in the first chromosomal region of the 2D query, up to about 10 times for chromosome 1.