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Oryza sativa Japonica Group vs Asparagus officinalis LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Asparagus officinalis (Asparagus officinalis, Aspof.V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 103. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterOryza sativa Japonica GroupAsparagus officinalis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 172,531 alignment blocks

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

Uncovered: 340,251,330 out of 375,049,285
Covered: 34,797,955 out of 375,049,285

Uncovered: 13,243,743 out of 34,424,450
Matches: 13,919,674 out of 34,424,450
Mismatches: 6,645,134 out of 34,424,450
Insertions: 615,899 out of 34,424,450
Identity over aligned base-pairs: 65.7%

Asparagus officinalis

Uncovered: 1,147,641,097 out of 1,187,538,024
Covered: 39,896,927 out of 1,187,538,024

Uncovered: 7,992,782 out of 24,293,357
Matches: 11,019,219 out of 24,293,357
Mismatches: 4,963,253 out of 24,293,357
Insertions: 318,103 out of 24,293,357
Identity over aligned base-pairs: 67.6%

Block size distribution

Size range All 172,531 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,033
4.9 kb
10 bp - 100 bp
28,898
2.1 Mb
9,833
720.2 kb
100 bp - 1 kb
134,093
41.8 Mb
52,717
19.0 Mb
1 kb - 10 kb
8,500
12.9 Mb
18,043
36.6 Mb
10 kb - 100 kb
7
103.2 kb
46
600.9 kb