Table 1:
Assembly quality score value statistics and structural inconsistencies measured between ARS-UCD1.2 and UMD3.1.1 using Dominette whole-genome sequencing reads
| Major category | Subcategory | ARS-UCD1.2 | UMD3.1.1 | Description |
|---|---|---|---|---|
| QV | 48.67 | 37.98 | Quality value estimate (Phred-scale) | |
| FRCbam | ||||
| COMPR PE | 37,309 (30,643)1 | 54,602 (52,606) | Areas with low CE statistics | |
| STRECH PE | 37,255 (22,741) | 35,766 (35,299) | Areas with high CE statistics | |
| HIGH COV PE | 7,166 (1,970) | 7,711 (6,331) | High read coverage areas (all aligned reads) | |
| HIGH NORM COV PE | 5,641 (1,125) | 7,109 (5,778) | High paired-read coverage areas (only properly aligned pairs) | |
| HIGH OUTIE PE | 139 (102) | 2,108 (2,108) | Regions with high numbers of misoriented or distant pairs | |
| HIGH SINGLE PE | 60 (53) | 1,258 (1,256) | Regions with high numbers of unmapped pairs | |
| HIGH SPAN PE | 4,882 (1,687) | 4,172 (3,582) | Regions with high numbers of pairs that map to different scaffolds | |
| LOW COV PE | 43,370 (36,062) | 57,176 (56,648) | Low read coverage areas (all aligned reads) | |
| LOW NORM COV PE | 42,067 (34,592) | 60,560 (59,926) | Low paired-end coverage areas (only properly aligned pairs) | |
| Total features | 177,889 (128,975) | 230,462 (223,534) | All erroneous features | |
| Sniffles2 | ||||
| DEL | 188 | 10,504 | Deletions | |
| DUP | 16 | 728 | Duplications | |
| INS | 106 | 4,911 | Insertions | |
| INV | 34 | 2,675 | Inversions | |
| Total SVs | 344 | 18,818 | All structural variants |
1
Numbers in parentheses indicate the errors in placed chromosome scaffolds only.
2
Sniffles structural variant (SV) calls were generated using long reads aligned to the whole assembly.
CE: compression/expansion; QV: quality value.