Arabidopsis thaliana vs Daucus carota LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Daucus carota (Daucus carota subsp. sativus, ASM162521v1) 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: 155,802

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

Uncovered: 85,951,759 out of 119,667,750
Covered: 33,715,991 out of 119,667,750

Uncovered: 9,477,353 out of 33,775,569
Matches: 16,227,530 out of 33,775,569
Mismatches: 7,510,755 out of 33,775,569
Insertions: 559,931 out of 33,775,569

Daucus carota subsp. sativus

Uncovered: 376,465,506 out of 421,502,825
Covered: 45,037,319 out of 421,502,825

Uncovered: 12,107,747 out of 38,118,360
Matches: 17,330,738 out of 38,118,360
Mismatches: 8,038,034 out of 38,118,360
Insertions: 641,841 out of 38,118,360

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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 Daucus carota
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}