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Table 4 Validation structural polymorphisms

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

Prediction Confirmation
SV Span size n CMP RE aamq Breed Breakpoints Size Size in RRL Breed
15 251 1 X   97 2 NA    
14 402 3    97 1,2 10_1627991-1628223 232 170 1,2
13 414 2    93 W NA    
18 640 1   X 99 1 NA    
22 661 121 X X 77 W,B,1,2 NA    
17 729 4 X   94 W,2 3_110574268-110574832 564 165 W,2
20 780 6   X 96 W,1,2 NA    
21 884 1 X X 99 1 NA    
19 970 2   X 99 1 NA    
25 1248 3    73 2 1_188914114-188915200 1086 162 B,1,2
23 1319 1    97 2 2_55356006-55357163 1157 162 1,2
24 1376 2    70 2 4_23256240-23257477 1237 139 W,B,1,2
26 5845 1 X   90 W 2_112569238-112574924 5686 159 W
27 19574 15 X   96 W,1 - - - -
28 8128 489 X   93 2 1_61836457_61844398 7941 187 W,B,1,2
50 64 48    71 B,1,2 2_152470660*    1,2
51 86 39    69 2 3_19576932 115 201 W,B,1,2
52 229 141    79 B,1,2 4_43663736-43663781 45 184 W,B,1,2
53 274 10    76 B,1,2 6_6687386-6687469 83 191 B,1,2
54 283 140 X   74 B,1,2 2_46860428-46860509 81 202 B,1,2
55 360 4    76 1 3_67474749-67474961 212 148 1
56 367 21 X   72 B 1_189692870-189693048 178 189 B
57 544 4    69 1,2 7_28561048-28561407 359 185 12
58 662 2    60 1 1_44948882-44949390 508 154 W,B,1,2
59 868 2 X   97 2 1_99177206-99177957 751 117 B,1,2
  1. Structural variants (SV) 13-18 were chosen before application of the empirical rule (span-size deviation) × n >500, whereas 50-59 were chosen after. Span size is the distance (in base pairs) on the reference sequence spanned by discordantly mapping read pairs. The number of observed discordantly mapping read pairs that support the presence of this structural variant is given by n. CMP is flagged in case there were also concordantly mapping read pairs observed in that particular genomic region. Discordantly mapping read pairs spanning an assembly problem in the reference genome are flagged in the RE column. The alternative mapping quality of a predicted SV is the average mapping quality calculated over discordantly mapping read pairs within a cluster. Deletion breakpoints are in the notation chr_start-stop, whereas insertion breakpoints are given in the notation chr_position. Not acquired (NA) breakpoints were due to false positive SV predictions whereas breakpoints for SV27 were not acquired for technical reasons and not accurately acquired in SV50 due to low sequence complexity. W = white egg layer; B = brown egg layer; 1 = broiler 1; 2 = broiler 2.
  2. *Due to the low sequence complexity, the exact location of insertion could not be revealed