Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

Table 3 Comparison of the mapping quality and distribution between concordantly and discordantly mapping read pairs

Chromosome	Number of mapping read pairs		Average mapping quality		Mapping density		RRL density
1	5329141	15630	67.92	69.11	38	12860	1148
2	3968343	15049	68.14	71.29	39	10291	1149
3	3344481	11031	68.87	68.20	34	10303	1119
4	2758645	8155	68.53	70.40	34	11555	1098
5	1975228	5390	68.53	67.93	32	11547	1065
6	1258393	2782	68.31	69.69	30	13443	1056
7	1336228	4669	68.78	65.41	29	8221	1053
8	1119526	2866	68.63	72.82	27	10702	1067
9	1016524	3232	68.16	69.65	25	7907	1028
10	761372	2725	68.20	69.52	30	8278	1044
11	677920	1381	68.56	68.70	32	15879	1050
12	864303	3039	68.33	69.74	24	6758	989
13	780565	2107	68.47	66.72	24	8976	966
14	740461	3512	67.86	69.36	21	4504	929
15	669260	1378	68.56	68.47	19	9411	916
20	722054	2501	68.78	68.27	19	5592	911
Z	1845751	11981	68.05	68.79	40	6227	1271

The number of concordant and discordant (in italics) mapping read pairs per chromosome are given. The average mapping quality of concordantly and discordantly mapping read pairs was calculated per chromosome. By calculating the mapping density, the distribution of mapping read pairs over the genome were evaluated. Mapping density was calculated by dividing the chromosome length by the number of concordantly/discordantly mapping read pairs. RRL density was calculated to ascertain the contribution of the RRL approach to differences in mapping density. RRL densities were calculated by dividing the chromosome length by the (in silico) estimated number of RRL fragments.

ISSN: 1471-2164