Oryza sativa Japonica Group vs Daucus carota LastZ Results

Back to all analyses

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Daucus carota (Daucus carota subsp. sativus, ASM162521v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 159,297

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 343,431,734 out of 375,049,285
Covered: 31,617,551 out of 375,049,285

Uncovered: 14,985,804 out of 34,403,043
Matches: 12,502,385 out of 34,403,043
Mismatches: 6,467,874 out of 34,403,043
Insertions: 446,980 out of 34,403,043

Daucus carota subsp. sativus

Uncovered: 384,509,919 out of 421,502,825
Covered: 36,992,906 out of 421,502,825

Uncovered: 15,930,827 out of 38,118,360
Matches: 14,427,445 out of 38,118,360
Mismatches: 7,329,232 out of 38,118,360
Insertions: 430,856 out of 38,118,360

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Oryza sativa Japonica Group Daucus carota
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}