Table 3 Mis-assembly comparison of the refined panda genome with SOAPdenovo-assembled genome
From: LDscaff: LD-based scaffolding of de novo genome assemblies
Assembly evaluation | Before LDscaff | After LDscaff |
|---|---|---|
Misassemblies | 1092 | 448 |
Contig misassemblies | 866 | 314 |
   c. relocations | 822 | 283 |
   c. translocations | 38 | 28 |
   c. inversions | 6 | 3 |
Scaffold misassemblies | 226 | 134 |
   s. relocations | 220 | 126 |
   s. translocations | 6 | 8 |
   s. inversions | 0 | 0 |
Misassembled contigs | 200 | 37 |
Misassembled contigs length | 211889858 | 104831721 |
Local misassemblies | 8122 | 2873 |
Scaffold gap ext. mis. | 71 | 21 |
Scaffold gap loc. mis. | 4856 | 1792 |
Unaligned mis. contigs | 1502 | 563 |
Mismatches | 412290 | 191921 |
Indels | 95351 | 46834 |
   Indels (\(\le\) 5 bp) | 67654 | 33342 |
   Indels (> 5 bp) | 27697 | 13492 |
Indels length | 896205 | 436349 |