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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