Table 5 Mis-assembly comparison of the refined donkey genome with SOAPdenovo-assembled genome
From: LDscaff: LD-based scaffolding of de novo genome assemblies
Assembly evaluation | Before LDscaff | After LDscaff |
|---|---|---|
Misassemblies | 7166 | 3266 |
Contig misassemblies | 5173 | 2330 |
   c. relocations | 1517 | 651 |
   c. translocations | 3319 | 1522 |
   c. inversions | 337 | 157 |
Scaffold misassemblies | 1993 | 936 |
   s. relocations | 425 | 215 |
   s. translocations | 1543 | 712 |
   s. inversions | 25 | 9 |
Misassembled contigs | 369 | 122 |
Misassembled contigs length | 2256451641 | 1112560100 |
Local misassemblies | 59490 | 26941 |
Scaffold gap ext. mis. | 80 | 31 |
Scaffold gap loc. mis. | 26321 | 12206 |
Unaligned mis. contigs | 18 | 26 |
Mismatches | 27642582 | 13299554 |
Indels | 2673003 | 1283993 |
   Indels (\(\le\) 5 bp) | 2189565 | 1051168 |
   Indels (> 5 bp) | 483438 | 232825 |
Indels length | 13686335 | 6581365 |