Arabidopsis thaliana vs Lupinus angustifolius LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Lupinus angustifolius (Lupinus angustifolius, LupAngTanjil_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: 189,232

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

Uncovered: 84,080,460 out of 119,667,750
Covered: 35,587,290 out of 119,667,750

Uncovered: 8,944,179 out of 33,775,569
Matches: 16,740,800 out of 33,775,569
Mismatches: 7,514,231 out of 33,775,569
Insertions: 576,359 out of 33,775,569

Lupinus angustifolius

Uncovered: 553,664,160 out of 609,203,021
Covered: 55,538,861 out of 609,203,021

Uncovered: 8,665,503 out of 42,631,353
Matches: 23,043,068 out of 42,631,353
Mismatches: 10,030,182 out of 42,631,353
Insertions: 892,600 out of 42,631,353

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 Lupinus angustifolius
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}