Table 2.
Arabidopsis genome assembly comparisons
| HGAP inbreds, Col-0 vs. Cvi-0 | Falcon Unzip haplotigs vs primary contigs | |||
|---|---|---|---|---|
| Variant Type | events | Affected Bases | events | Affected Bases |
| SNP Count | 501,243 | 1,002,486 | 450,680 | 901,360 |
| indel > 50 bp | 1,051 | 882,736 | 966 | 798,438 |
| repeat contraction/expansion > 50 bp | 1,670 | 3,746,572 | 1,479 | 3,130,205 |
| tandem contraction/expansion > 50 bp | 73 | 97,319 | 65 | 85,495 |
| total SV > 50 bp detected | 2,794 | 4,726,627 | 2,510 | 4,014,138 |
| predicted CDS | Col-0:28,176, Cvi-0:27,797 | p:31,679, h:24,808 | ||
| Aligned CDS pairs | 27,424 | 24,808 | ||
| predicted coding sequence SNPs | 183,942 | 367,884 | 147,811 | 295,622 |
| other predicted coding sequence variants | 16,748 | 153,260 | 15,151 | 136,245 |
| local in-frame variants | 5,135 | 82,929 | 4,090 | 66,681 |
| local non in-frame variants | 11,613 | 70,331 | 11,061 | 69,564 |