Oryza meridionalis vs Oryza glaberrima LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza meridionalis 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 meridionalisOryza glaberrima
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 263,514 alignment blocks

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

Uncovered: 136,108,439 out of 335,668,232
Covered: 199,559,793 out of 335,668,232

Uncovered: 1,551,351 out of 35,224,824
Matches: 31,831,704 out of 35,224,824
Mismatches: 1,525,906 out of 35,224,824
Insertions: 315,863 out of 35,224,824
Identity over aligned base-pairs: 94.5%

Oryza glaberrima

Uncovered: 144,427,094 out of 316,419,574
Covered: 171,992,480 out of 316,419,574

Uncovered: 7,497,953 out of 36,293,721
Matches: 27,937,921 out of 36,293,721
Mismatches: 690,976 out of 36,293,721
Insertions: 166,871 out of 36,293,721
Identity over aligned base-pairs: 97.0%