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Oryza sativa Japonica Group vs Lupinus angustifolius LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Lupinus angustifolius (Lupinus angustifolius, LupAngTanjil_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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 GroupLupinus angustifolius
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 182,731 alignment blocks

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

Uncovered: 343,116,660 out of 375,049,285
Covered: 31,932,625 out of 375,049,285

Uncovered: 15,372,919 out of 34,403,043
Matches: 12,267,619 out of 34,403,043
Mismatches: 6,335,632 out of 34,403,043
Insertions: 426,873 out of 34,403,043
Identity over aligned base-pairs: 64.5%

Lupinus angustifolius

Uncovered: 565,310,993 out of 609,203,021
Covered: 43,892,028 out of 609,203,021

Uncovered: 14,453,846 out of 42,631,353
Matches: 18,538,668 out of 42,631,353
Mismatches: 9,096,068 out of 42,631,353
Insertions: 542,771 out of 42,631,353
Identity over aligned base-pairs: 65.8%

Block size distribution

Size range All 182,731 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,537
7.4 kb
10 bp - 100 bp
30,396
2.1 Mb
6,644
476.7 kb
100 bp - 1 kb
142,108
44.4 Mb
38,845
14.9 Mb
1 kb - 10 kb
8,689
12.8 Mb
20,390
43.3 Mb
10 kb - 100 kb
1
13.6 kb
53
681.8 kb