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Table 4 Sequence variation of DOP-PCR amplified chromosome-specific DNA relative to bosTau7 genome classified relative to bovine RefSeq genes

From: Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosome-specific DNA sequencing

  BTAMix CPYB CPYB-CCA MGOB
A
Total 6,068,678 344,775 297,042 1,332,441
Intergenic 4,518,518 262,448 226,421 991,640
Intron 1,501,565 80,987 69,282 327,012
5` UTR 1,337 0 0 27
3` UTR 15,213 0 0 2,780
Coding 32,045 1,340 1,339 10,982
B
Total 19188 (6374) 15267 (2915) 3086 (1929) 46592 (1735)
Intergenic 14829 (4970) 12187 (2349) 2476 (1530) 35292 (1334)
Intron 4556 (1474) 3134 (558) 605 (392) 10102 (320)
5` UTR 4 (2) - - 2 (0)
3` UTR 49 (18) - - 101 (8)
Coding syn. 46 (8) 17 (3) 1 (1) 113 (2)
Coding non-syn. 44 (15) 26 (10) 12 (9) 103 (12)
C
Total 316 (952) 23 (118) 96 (154) 29 (768)
Intergenic 305 (909) 22 (112) 91 (148) 28 (743)
Intron 330 (1,019) 26 (145) 115 (177) 32 (1,022)
5` UTR 334 (669) - - 14 (-)
3` UTR 310 (845) - - 28 (348)
Coding 356 (1,393) 31 (103) 103 (134) 51 (732)
  1. A. Lengths of cattle genome regions covered by reads. Samples: BTAMix – mixed peak of cattle chromosomes 23, 26, 28 and 29; CPYB – Siberian roe deer B chromosomes (combination of samples CPYB1 and CPYB2); CPYB-CCA – same, but regions not covered by European roe deer contigs are excluded; MGOB – grey brocket deer B chromosomes
  2. B. Number of total and heterozygous (in brackets) variants called and their annotation. Numbers of variants do not add up due to overlapping annotations and excluded NMD_target_transcript annotation. Intergenic variants also include up/downstream variants; coding non-synonymous variants include missense, stop codon gain/loss, frameshift, inframe indels. Sample descriptions – see 3A, except for CPYB-CCA – CPYB variants excluding the variants observed in Capreolus capreolus genomic contigs
  3. C. Variant density (bp per 1 variant) calculated as length of sequence covered by reads divided by number of called variants. Numbers are given for all and heterozygous (in brackets) variants. Sample descriptions – see 3B