Skip to main content

Table 1 BAC-end sequence (BES) characteristics

From: Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)

Annotation Retro-element
(RE)
Genes
(G)
G + RE Transposable
elements (TE)
G + TE Non-annotated
(NA)
Totals
Total ends 17928 17255 2,566 327 148 44,157 82,381
Total unique clusters a 7,401 11,233 913 201 44 32,147 51,939
Average cluster depth 2.42 1.54 2.81 1.63 3.36 1.37 1.69
Total unique sequence b 58,25,082 81,60,879 7,59,831 1,54,620 44,218 2,02,54,481 3,51,99,111
Total clusters with SSRs 302 1,083 13 11 0 3,188 4,597
Total SSRs 593 1,483 21 15 0 4100 6,212
SSRs/100 Kbp 10.2 18.2 2.8 9.7 0 20 17.7
Selected SSR-BESs d 124 646 4 2 0 1943 2,719
Polymorphic SSRs c 32 241 0 0 0 568 839
Average number of alleles 5.0 ± 1.7 5.4 ± 1.7 na na na 5.8 ± 2.1 5.7 ± 2.0
Average PIC value 0.53 ± 0.20 0.58 ± 0.18 na na na 0.57 ± .19 0.57 ± 0.18
  1. aTotal unique clusters represent the total number of sequence clusters plus the number of singleton (non-clustered) sequences.
  2. bTotal unique sequence represents the sum of the nucleotide length of all unique sequence clusters.
  3. cThree polymorphic markers are from BAC ends annotated as "chloroplast" and are not listed in this table.
  4. d2,964 SSR markers were derived from 2,719 BESs, with some BESs containing multiple SSRs