Arabidopsis thaliana vs Oryza meridionalis LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Arabidopsis thaliana 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

ParameterArabidopsis thalianaOryza meridionalis
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 81,300 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,464,142 out of 119,667,750
Covered: 26,203,608 out of 119,667,750

Uncovered: 13,938,754 out of 33,462,323
Matches: 12,729,439 out of 33,462,323
Mismatches: 6,422,368 out of 33,462,323
Insertions: 371,762 out of 33,462,323
Identity over aligned base-pairs: 65.2%

Oryza meridionalis

Uncovered: 317,605,720 out of 335,668,232
Covered: 18,062,512 out of 335,668,232

Uncovered: 23,365,963 out of 35,394,330
Matches: 7,791,568 out of 35,394,330
Mismatches: 3,937,279 out of 35,394,330
Insertions: 299,520 out of 35,394,330
Identity over aligned base-pairs: 64.8%