Arabidopsis thaliana vs Rosa chinensis LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Rosa chinensis (Rosa chinensis, RchiOBHm-V2) 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: 176,523

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

Uncovered: 83,284,751 out of 119,667,750
Covered: 36,382,999 out of 119,667,750

Uncovered: 8,106,481 out of 33,775,569
Matches: 17,449,044 out of 33,775,569
Mismatches: 7,649,364 out of 33,775,569
Insertions: 570,680 out of 33,775,569

Rosa chinensis

Uncovered: 463,078,403 out of 515,588,973
Covered: 52,510,570 out of 515,588,973

Uncovered: 14,400,042 out of 43,773,732
Matches: 19,595,053 out of 43,773,732
Mismatches: 8,961,557 out of 43,773,732
Insertions: 817,080 out of 43,773,732

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 Rosa chinensis
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options