Arabidopsis thaliana vs Oryza sativa Indica LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza sativa Indica (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 119,378

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

Uncovered: 93,204,588 out of 119,667,750
Covered: 26,463,162 out of 119,667,750

Uncovered: 14,250,221 out of 33,775,569
Matches: 12,685,684 out of 33,775,569
Mismatches: 6,450,770 out of 33,775,569
Insertions: 388,894 out of 33,775,569

Oryza sativa Indica Group

Uncovered: 396,245,759 out of 427,004,890
Covered: 30,759,131 out of 427,004,890

Uncovered: 24,597,243 out of 45,465,969
Matches: 13,396,390 out of 45,465,969
Mismatches: 6,971,101 out of 45,465,969
Insertions: 501,235 out of 45,465,969

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Arabidopsis thaliana Oryza sativa Indica
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}