Oryza glaberrima vs Oryza brachyantha LastZ results

Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 67. Oryza glaberrima 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

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)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterOryza glaberrimaOryza brachyantha
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 226,574 alignment blocks

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

Uncovered: 170,501,788 out of 285,037,524
Covered: 114,535,736 out of 285,037,524

Uncovered: 4,210,900 out of 36,404,702
Matches: 27,408,119 out of 36,404,702
Mismatches: 4,059,029 out of 36,404,702
Insertions: 726,654 out of 36,404,702
Identity over aligned base-pairs: 85.1%

Oryza brachyantha

Uncovered: 156,413,234 out of 250,927,218
Covered: 94,513,984 out of 250,927,218

Uncovered: 5,427,841 out of 30,210,943
Matches: 21,927,619 out of 30,210,943
Mismatches: 2,475,300 out of 30,210,943
Insertions: 380,183 out of 30,210,943
Identity over aligned base-pairs: 88.5%