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Oryza sativa Japonica Group vs Helianthus annuus LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Helianthus annuus (Helianthus annuus, HanXRQr1.0) 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 GroupHelianthus annuus
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 229,529 alignment blocks

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

Uncovered: 341,316,294 out of 375,049,285
Covered: 33,732,991 out of 375,049,285

Uncovered: 14,833,725 out of 34,403,043
Matches: 12,371,582 out of 34,403,043
Mismatches: 6,659,935 out of 34,403,043
Insertions: 537,801 out of 34,403,043
Identity over aligned base-pairs: 63.2%

Helianthus annuus

Uncovered: 2,974,593,597 out of 3,027,844,945
Covered: 53,251,348 out of 3,027,844,945

Uncovered: 22,768,609 out of 54,343,734
Matches: 20,544,999 out of 54,343,734
Mismatches: 10,464,606 out of 54,343,734
Insertions: 565,520 out of 54,343,734
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 229,529 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,511
7.2 kb
10 bp - 100 bp
41,459
2.9 Mb
14,162
1.0 Mb
100 bp - 1 kb
178,226
53.4 Mb
68,947
24.6 Mb
1 kb - 10 kb
8,248
14.1 Mb
21,616
42.7 Mb
10 kb - 100 kb
85
944.1 kb
177
3.0 Mb