Table 2.

Summary of sequence alignment to the human genome

Sample	Reads to align a	Reads aligned to genome	Percentage b	Reads properly paired	Percentage c	Reads with mate unmapped	Percentage d	Percentage of ‘expressed’ genes e
Young 1	61,516,106	55,995,223	91.03	51,821,068	92.55	4,174,155	7.45	46.65
Young 2	74,068,430	67,565,304	91.22	62,477,226	92.47	5,088,078	7.53	45.98
Young 3	65,954,168	60,771,423	92.14	56,659,046	93.23	4,112,377	6.77	47.19
Young 4	59,947,540	53,381,917	89.05	48,909,710	91.62	4,472,207	8.38	40.58
Young 5	89,707,092	80,798,459	90.07	74,516,846	92.23	6,281,613	7.77	45.01
Old 1	62,712,522	57,345,261	91.44	53,413,212	93.14	3,932,049	6.86	46.42
Old 2	46,590,704	41,788,780	89.69	38,331,156	91.73	3,457,624	8.27	40.46
Old 3	61,364,402	55,643,829	90.68	51,415,610	92.40	4,228,219	7.60	46.36
Old 4	55,361,082	49,725,122	89.82	45,615,238	91.73	4,109,884	8.27	42.44
Maximum	89,707,092	80,798,459	92.14	74,516,846	93.23	6,281,613	8.38	47.4
Mean	65,591,734	59,482,205	90.65	54,953,876	92.36	4,528,330	7.64	44.92
Minimum	46,590,704	41,788,780	89.05	38,331,156	91.62	3,457,624	6.77	40.46

The table shows the number and percentage of reads mapped to the human reference sequences. ^aSum of R1 and R2 reads used in the alignment. ^bPercentage of reads used in the alignment that align to the reference genome. ^cPercentage of reads used in the alignment that align to the reference genome in the correct relative orientation to their mate. ^dPercentage of reads used in the alignment that align to the reference genome but whose mate does not align. ^ePercentage of 63,152 annotated human genes with at least one read aligned.