Oryza sativa Japonica Group vs Coffea canephora LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Coffea canephora (Coffea canephora str. DH200-94, AUK_PRJEB4211_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 133,289

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 342,625,991 out of 375,049,285
Covered: 32,423,294 out of 375,049,285

Uncovered: 14,773,187 out of 34,424,450
Matches: 12,634,853 out of 34,424,450
Mismatches: 6,589,682 out of 34,424,450
Insertions: 426,728 out of 34,424,450

Coffea canephora str. DH200-94

Uncovered: 538,200,691 out of 568,611,505
Covered: 30,410,814 out of 568,611,505

Uncovered: 11,467,833 out of 30,830,841
Matches: 12,504,343 out of 30,830,841
Mismatches: 6,432,482 out of 30,830,841
Insertions: 426,183 out of 30,830,841

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

Oryza sativa Japonica Group 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}