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Arabidopsis thaliana vs Oryza glumipatula LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) 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.


Number of alignment blocks: 110,861

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

Uncovered: 92,047,933 out of 119,667,750
Covered: 27,619,817 out of 119,667,750

Uncovered: 14,297,970 out of 33,775,569
Matches: 12,291,657 out of 33,775,569
Mismatches: 6,808,824 out of 33,775,569
Insertions: 377,118 out of 33,775,569

Oryza glumipatula

Uncovered: 343,539,197 out of 372,860,283
Covered: 29,321,086 out of 372,860,283

Uncovered: 21,538,641 out of 41,246,944
Matches: 12,652,148 out of 41,246,944
Mismatches: 6,570,124 out of 41,246,944
Insertions: 486,031 out of 41,246,944

Configuration parameters

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)
     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 glumipatula
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}