. 2018 Dec 26;168(3):496–509. doi: 10.1002/ajpa.23763

Table 2.

Reads mapping to sex chromosomes in precapture and postcapture libraries from 5 M dataset

Sample	Precapture				Postcapture
Sample	X + Y^a	Ry^b	SE	Sex^c	X + Y^a	Ry^b	SE	Sex^c
Calculus
C53	8	n.d.	n.d.	n.d.	54	n.d.	n.d.	n.d.
C214	11	n.d.	n.d.	n.d.	25	0.040	0.039	Female^d
S108	19	0.158	0.084	Male^d	73	0.055	0.027	Male^d
S454	279	0.118	0.019	Male^d	447	0.119	0.015	Male^d
F349A	6	n.d.	n.d.	n.d.	34	0.118	0.055	Male^d
F1948	20	n.d.	n.d.	n.d.	45	n.d.	n.d.	n.d.
NF47	64	n.d.	n.d.	n.d.	274	0.007	0.005	Female^d
NF217	65	0.154	0.045	Male^d	327	0.107	0.017	Male^d
H10	44	0.091	0.043	Male^d	146	0.151	0.030	Male^d
H24	14	0.071	0.069	Male^d	33	0.182	0.067	Male^d
S40	34	n.d.	n.d.	n.d.	66	0.015	0.015	Female^d
S41	207	0.087	0.020	Male^d	892	0.148	0.012	Male^d
Dentine
C53	25,168	0.004	0.001	Female	40,096	0.013	0.001	Female
C214	93	0.022	0.015	Female^d	151	0.026	0.013	Female^d
S108	5,141	0.096	0.004	Male	4,765	0.117	0.005	Male
S454	35	0.086	0.047	Male^d	33	0.151	0.062	Male^d
F349A	1,142	0.096	0.009	Male^d	955	0.157	0.012	Male^d
F1948	4,404	0.005	0.001	Female	16,675	0.009	0.001	Female
NF47	1,493	0.009	0.002	Female^d	4,144	0.015	0.002	Female
NF217	121	0.099	0.027	Male^d	454	0.121	0.015	Male^d
H10	34,928	0.096	0.002	Male	36,034	0.129	0.002	Male
H24	10,014	0.095	0.003	Male	10,668	0.134	0.003	Male
S40	10,719	0.004	0.001	Female	31,031	0.012	0.001	Female
S41	66,225	0.093	0.001	Male	64,243	0.116	0.001	Male

Total number of reads mapping to the sex chromosomes after removing PCR duplicates and reads with mapping quality <30.

Ry observed fraction of Y chromosome alignments compared with the total number of alignments to the X and Y chromosome (Skoglund et al., 2013).

Typical Ry for males is an Ry over 0.09. Ry values under 0.02 are considered female.

Sex predicted by Ry value, but insufficient X + Y reads are available for confident assignment. A minimum of 3,000 R + Y reads are recommended for sex assignment (Skoglund et al., 2013).