Oryza nivara vs Leersia perrieri LastZ Results

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Oryza nivara (Oryza nivara, AWHD00000000) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza nivara 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: 243,632

Genome coverage (bp) Coding exon coverage (bp)
Oryza nivara

Uncovered: 199,579,566 out of 337,950,324
Covered: 138,370,758 out of 337,950,324

Uncovered: 3,417,741 out of 42,480,949
Matches: 32,963,070 out of 42,480,949
Mismatches: 5,111,013 out of 42,480,949
Insertions: 989,125 out of 42,480,949

Leersia perrieri

Uncovered: 151,121,121 out of 266,687,832
Covered: 115,566,711 out of 266,687,832

Uncovered: 4,863,470 out of 36,899,367
Matches: 27,856,985 out of 36,899,367
Mismatches: 3,611,031 out of 36,899,367
Insertions: 567,881 out of 36,899,367

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 nivara Leersia perrieri
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}