Arabidopsis thaliana vs Corchorus capsularis LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Corchorus capsularis (Corchorus capsularis, CCACVL1_1.0) 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: 118,607

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

Uncovered: 82,227,722 out of 119,667,750
Covered: 37,440,028 out of 119,667,750

Uncovered: 7,786,763 out of 33,775,569
Matches: 17,871,759 out of 33,775,569
Mismatches: 7,565,227 out of 33,775,569
Insertions: 551,820 out of 33,775,569

Corchorus capsularis

Uncovered: 279,948,606 out of 317,178,409
Covered: 37,229,803 out of 317,178,409

Uncovered: 9,338,364 out of 30,371,305
Matches: 14,346,709 out of 30,371,305
Mismatches: 6,085,711 out of 30,371,305
Insertions: 600,521 out of 30,371,305

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 Corchorus capsularis
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}