Arabidopsis thaliana vs Oryza rufipogon LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 113,206

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,573,917 out of 119,667,750
Covered: 26,093,833 out of 119,667,750

Uncovered: 14,489,656 out of 33,775,569
Matches: 12,521,884 out of 33,775,569
Mismatches: 6,379,404 out of 33,775,569
Insertions: 384,625 out of 33,775,569

Oryza rufipogon

Uncovered: 309,346,329 out of 338,040,714
Covered: 28,694,385 out of 338,040,714

Uncovered: 22,634,884 out of 42,763,723
Matches: 12,914,679 out of 42,763,723
Mismatches: 6,715,139 out of 42,763,723
Insertions: 499,021 out of 42,763,723

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

Arabidopsis thaliana Oryza rufipogon
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}