Arabidopsis thaliana vs Dioscorea rotundata LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Dioscorea rotundata (Dioscorea rotundata, TDr96_F1_Pseudo_Chromosome_v1.0) 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: 116,950

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

Uncovered: 89,360,836 out of 119,667,750
Covered: 30,306,914 out of 119,667,750

Uncovered: 12,654,341 out of 33,775,569
Matches: 13,547,854 out of 33,775,569
Mismatches: 7,084,714 out of 33,775,569
Insertions: 488,660 out of 33,775,569

Dioscorea rotundata

Uncovered: 423,712,218 out of 456,674,974
Covered: 32,962,756 out of 456,674,974

Uncovered: 8,844,775 out of 24,441,241
Matches: 10,216,349 out of 24,441,241
Mismatches: 4,988,478 out of 24,441,241
Insertions: 391,639 out of 24,441,241

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 Dioscorea rotundata
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}