Oryza sativa Japonica Group vs Vigna radiata LastZ Results

Back to all analyses

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Vigna radiata (Vigna radiata var. radiata, Vradiata_ver6) 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: 155,870

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

Uncovered: 341,429,803 out of 375,049,285
Covered: 33,619,482 out of 375,049,285

Uncovered: 14,059,288 out of 34,403,043
Matches: 13,074,671 out of 34,403,043
Mismatches: 6,747,687 out of 34,403,043
Insertions: 521,397 out of 34,403,043

Vigna radiata var. radiata

Uncovered: 427,352,416 out of 463,085,359
Covered: 35,732,943 out of 463,085,359

Uncovered: 13,007,149 out of 36,130,572
Matches: 15,061,205 out of 36,130,572
Mismatches: 7,573,091 out of 36,130,572
Insertions: 489,127 out of 36,130,572

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
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 Vigna radiata
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}