Arabidopsis thaliana vs Manihot esculenta LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Manihot esculenta (Manihot esculenta, Manihot_esculenta_v6) 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: 151,801

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

Uncovered: 80,973,383 out of 119,667,750
Covered: 38,694,367 out of 119,667,750

Uncovered: 7,421,507 out of 33,775,569
Matches: 17,742,499 out of 33,775,569
Mismatches: 8,048,240 out of 33,775,569
Insertions: 563,323 out of 33,775,569

Manihot esculenta

Uncovered: 533,737,641 out of 582,117,524
Covered: 48,379,883 out of 582,117,524

Uncovered: 8,222,757 out of 38,679,430
Matches: 20,650,995 out of 38,679,430
Mismatches: 8,948,826 out of 38,679,430
Insertions: 856,852 out of 38,679,430

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 Manihot esculenta
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}