Oryza glaberrima vs Oryza longistaminata LastZ results

Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) and Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. 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 longistaminata
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 300,823 alignment blocks

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

Uncovered: 83,636,330 out of 316,419,574
Covered: 232,783,244 out of 316,419,574

Uncovered: 1,923,055 out of 36,293,721
Matches: 32,367,683 out of 36,293,721
Mismatches: 1,623,948 out of 36,293,721
Insertions: 379,035 out of 36,293,721
Identity over aligned base-pairs: 94.2%

Oryza longistaminata

Uncovered: 135,882,283 out of 326,442,508
Covered: 190,560,225 out of 326,442,508

Uncovered: 7,032,661 out of 34,512,301
Matches: 26,686,445 out of 34,512,301
Mismatches: 675,177 out of 34,512,301
Insertions: 118,018 out of 34,512,301
Identity over aligned base-pairs: 97.1%