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Oryza sativa Japonica Group vs Capsicum annuum LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Capsicum annuum (Capsicum annuum, ASM51225v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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 GroupCapsicum annuum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 191,256 alignment blocks

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

Uncovered: 344,375,458 out of 375,049,285
Covered: 30,673,827 out of 375,049,285

Uncovered: 15,729,866 out of 34,818,902
Matches: 12,204,818 out of 34,818,902
Mismatches: 6,471,833 out of 34,818,902
Insertions: 412,385 out of 34,818,902
Identity over aligned base-pairs: 63.9%

Capsicum annuum

Uncovered: 3,019,723,690 out of 3,063,864,880
Covered: 44,141,190 out of 3,063,864,880

Uncovered: 17,327,991 out of 39,113,865
Matches: 14,165,326 out of 39,113,865
Mismatches: 7,213,030 out of 39,113,865
Insertions: 407,518 out of 39,113,865
Identity over aligned base-pairs: 65.0%

Block size distribution

Size range All 191,256 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,130
5.4 kb
10 bp - 100 bp
34,451
2.5 Mb
12,492
906.9 kb
100 bp - 1 kb
147,548
44.3 Mb
60,741
21.6 Mb
1 kb - 10 kb
8,122
12.7 Mb
18,070
35.3 Mb
10 kb - 100 kb
5
76.0 kb
105
1.7 Mb