Oryza sativa Japonica vs Lupinus angustifolius LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Lupinus angustifolius (Lupinus angustifolius, LupAngTanjil_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica 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: 183,457

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

Uncovered: 342,926,415 out of 375,049,285
Covered: 32,122,870 out of 375,049,285

Uncovered: 15,271,535 out of 34,403,043
Matches: 12,327,485 out of 34,403,043
Mismatches: 6,372,532 out of 34,403,043
Insertions: 431,491 out of 34,403,043

Lupinus angustifolius

Uncovered: 565,325,861 out of 609,203,021
Covered: 43,877,160 out of 609,203,021

Uncovered: 6,152,804 out of 18,016,600
Matches: 7,807,468 out of 18,016,600
Mismatches: 3,824,844 out of 18,016,600
Insertions: 231,484 out of 18,016,600

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 Lupinus angustifolius
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}