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Oryza sativa Japonica Group vs Beta vulgaris LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Beta vulgaris (Beta vulgaris subsp. vulgaris, RefBeet-1.2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 GroupBeta vulgaris
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 123,504 alignment blocks

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

Uncovered: 345,716,257 out of 375,049,285
Covered: 29,333,028 out of 375,049,285

Uncovered: 16,300,113 out of 34,403,043
Matches: 11,641,764 out of 34,403,043
Mismatches: 6,093,203 out of 34,403,043
Insertions: 367,963 out of 34,403,043
Identity over aligned base-pairs: 64.3%

Beta vulgaris

Uncovered: 540,827,117 out of 566,181,630
Covered: 25,354,513 out of 566,181,630

Uncovered: 12,325,855 out of 28,257,705
Matches: 10,334,427 out of 28,257,705
Mismatches: 5,287,948 out of 28,257,705
Insertions: 309,475 out of 28,257,705
Identity over aligned base-pairs: 64.9%

Block size distribution

Size range All 123,504 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
708
3.4 kb
1
1.0 bp
10 bp - 100 bp
20,630
1.5 Mb
6,062
441.1 kb
100 bp - 1 kb
96,757
29.5 Mb
32,125
12.0 Mb
1 kb - 10 kb
5,367
8.1 Mb
13,026
26.2 Mb
10 kb - 100 kb
42
767.3 kb
70
1.2 Mb