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Arabidopsis thaliana vs Coffea canephora LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Coffea canephora (Coffea canephora str. DH200-94, AUK_PRJEB4211_v1) 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.


Number of alignment blocks: 128,536

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

Uncovered: 86,401,346 out of 119,667,750
Covered: 33,266,404 out of 119,667,750

Uncovered: 9,533,609 out of 33,775,569
Matches: 16,105,174 out of 33,775,569
Mismatches: 7,671,052 out of 33,775,569
Insertions: 465,734 out of 33,775,569

Coffea canephora str. DH200-94

Uncovered: 533,444,799 out of 568,611,505
Covered: 35,166,706 out of 568,611,505

Uncovered: 9,216,946 out of 30,830,841
Matches: 14,344,990 out of 30,830,841
Mismatches: 6,709,828 out of 30,830,841
Insertions: 559,077 out of 30,830,841

Configuration parameters

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)
     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 Coffea canephora
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}