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Oryza rufipogon vs Leersia perrieri LastZ results

Oryza rufipogon (Oryza rufipogon, OR_W1943) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza rufipogon 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 rufipogonLeersia perrieri
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 253,725 alignment blocks

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

Uncovered: 198,926,311 out of 338,040,714
Covered: 139,114,403 out of 338,040,714

Uncovered: 3,702,880 out of 42,764,129
Matches: 32,951,662 out of 42,764,129
Mismatches: 5,128,420 out of 42,764,129
Insertions: 981,167 out of 42,764,129
Identity over aligned base-pairs: 84.4%

Leersia perrieri

Uncovered: 150,785,574 out of 266,687,832
Covered: 115,902,258 out of 266,687,832

Uncovered: 4,755,670 out of 36,899,367
Matches: 27,936,595 out of 36,899,367
Mismatches: 3,628,317 out of 36,899,367
Insertions: 578,785 out of 36,899,367
Identity over aligned base-pairs: 86.9%