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

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

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
  1. 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.