Arabidopsis thaliana vs Vigna angularis LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Vigna angularis (Vigna angularis, Vigan1.1) 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: 144,816

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

Uncovered: 85,295,260 out of 119,667,750
Covered: 34,372,490 out of 119,667,750

Uncovered: 9,180,667 out of 33,775,569
Matches: 16,530,954 out of 33,775,569
Mismatches: 7,495,942 out of 33,775,569
Insertions: 568,006 out of 33,775,569

Vigna angularis

Uncovered: 425,879,610 out of 466,744,453
Covered: 40,864,843 out of 466,744,453

Uncovered: 13,689,796 out of 37,822,470
Matches: 16,178,761 out of 37,822,470
Mismatches: 7,345,848 out of 37,822,470
Insertions: 608,065 out of 37,822,470

Configuration parameters

ParameterValue
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)
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 Vigna angularis
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}