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Oryza nivara vs Leersia perrieri LastZ results

Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza nivara was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterOryza nivaraLeersia perrieri
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 243,632 alignment blocks

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
Identity over aligned base-pairs: 84.4%

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
Identity over aligned base-pairs: 87.0%