Arabidopsis thaliana vs Cannabis sativa female LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Cannabis sativa female (Cannabis sativa, cs10) 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: 125,811

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

Uncovered: 83,414,847 out of 119,667,750
Covered: 36,252,903 out of 119,667,750

Uncovered: 8,926,447 out of 33,775,569
Matches: 16,761,332 out of 33,775,569
Mismatches: 7,572,625 out of 33,775,569
Insertions: 515,165 out of 33,775,569

Cannabis sativa

Uncovered: 836,074,529 out of 875,732,045
Covered: 39,657,516 out of 875,732,045

Uncovered: 13,689,392 out of 33,180,649
Matches: 13,116,019 out of 33,180,649
Mismatches: 5,811,261 out of 33,180,649
Insertions: 563,977 out of 33,180,649

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 Cannabis sativa female
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options