Table 1. Summary statistics of data obtained using two different sequencing approaches: Illumina (RAD-seq) and 454 (shotgun).
| Feature | Illumina RAD-sequencing | 454 shotgun sequencing | ||||||||
| samples (n = 8) | samples (n = 2) | |||||||||
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | A | B | |
| Reads (millions) | 1.84 | 2.32 | 2.54 | 2.59 | 2.17 | 1.05 | 2.53 | 1.26 | 0.51 | 0.64 |
| Aligned reads between samples (%) | – | – | – | – | – | – | – | – | 219,157 (19.17%) | |
| Mb of sequence | 221.13 | 278 | 305.01 | 311.12 | 259.92 | 125.74 | 303.47 | 150.95 | – | |
| Total number of RAD tags produced (approximate) | 33,698 | 32,330 | 32,937 | 35,014 | 34,815 | 23,532 | 37,362 | 28,573 | – | |
| Total Mb of sequence after contig construction | – | 2.88 | – | 2.68 | – | – | 2.07 | 1.50 | – | |
| Contigs assembled | – | 10,008 | 10,110 | 10,352 | – | – | 7,918 | 5,461 | 16,857 (>100 bp) | |
| Average contig length (bp) | – | 288 | – | 259 | – | – | 262 | 275 | 328.13 | |
| Average depth of coverage per base of contigs | 12.9x | 8x | ||||||||
| N50*(bp) | – | 320 | – | 279 | – | – | 281 | 302 | 815 | |
| Contig length range(bp, min-max) | – | 150–560 | – | 150–457 | – | – | 150–544 | 150–527 | 100–6,407 | |
| Reads mapped to L. africana | – | – | – | – | – | – | – | – | 497,169 (97.6%) | 617,930 (97.2%) |
| Putative SNPs | 14,724 | 6,683 | ||||||||
| Total number of homozygotes (monomorphic) | 9,676 | – | ||||||||
| Total number of heterozygotes | 5,048 (34%) | – | ||||||||
| Transitions and transversions(Ts/Tv ratio) | 1.61 | 1.52 | ||||||||
| Candidate loci containing SNPs | 20%(2,100 out of 10,352) | 10%(1,753 out of 16,857) | ||||||||
| Loci suitable for Sequenom assay with >q20# and identified assays | 518 (24.6%),19 | 1,695 (96.6%), 52 | ||||||||
| SNP density | 0.00081 | 0.00056 | ||||||||
| Validation of SNPs(genotyping success rate acrossfive plexes) | 86–95%(plex1–plex4) | 91%(plex5) | ||||||||
| Polymorphic loci(n = 194) | 28 (E.m.borneensis), 17 (E.m.indicus) | 5 (E.m.borneensis), 7 (E.m.indicus) | ||||||||
| Number of contigs containing microsatellite loci | 837 | 18,195 | ||||||||
| Number of SSRs identified(mono-,di-,tri, and tetra-nucleotides) | 868(844 mono-, and 24 di-nucleotides)$ | 9,038(18,188,7,241, 1,471, 326) | ||||||||
| Potential amplifiable loci(with ≥3 repeats) | 7 (29%) | 1,706 (18.8%) | ||||||||
Note that the eight elephant samples (1 to 8) used in Illumina RAD-sequencing are different from the two.
samples (A and B) used in 454 shotgun sequencing.
*
weighted median statistic such that 50% of the entire assembly is contained in the number of contigs equal.
to or greater than this value.
#
>q20: 0.01% chance that a base was wrongly called.
$
identified in elephant sample 4.