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Oryza sativa Japonica Group vs Phaseolus vulgaris LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Phaseolus vulgaris (Phaseolus vulgaris, PhaVulg1_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 GroupPhaseolus 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 141,870 alignment blocks

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

Uncovered: 342,160,241 out of 375,049,285
Covered: 32,889,044 out of 375,049,285

Uncovered: 14,298,452 out of 34,403,043
Matches: 12,983,972 out of 34,403,043
Mismatches: 6,603,253 out of 34,403,043
Insertions: 517,366 out of 34,403,043
Identity over aligned base-pairs: 64.6%

Phaseolus vulgaris

Uncovered: 488,729,557 out of 521,076,696
Covered: 32,347,139 out of 521,076,696

Uncovered: 12,495,034 out of 34,663,348
Matches: 14,482,977 out of 34,663,348
Mismatches: 7,216,935 out of 34,663,348
Insertions: 468,402 out of 34,663,348
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 141,870 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,058
4.9 kb
10 bp - 100 bp
22,437
1.6 Mb
4,940
353.6 kb
100 bp - 1 kb
111,007
35.7 Mb
30,797
12.3 Mb
1 kb - 10 kb
7,353
11.0 Mb
17,020
35.2 Mb
10 kb - 100 kb
15
186.3 kb
53
672.8 kb