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Oryza sativa Japonica Group vs Sorghum bicolor LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) 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 GroupSorghum bicolor
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 187,234 alignment blocks

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

Uncovered: 298,485,504 out of 375,049,285
Covered: 76,563,781 out of 375,049,285

Uncovered: 3,435,785 out of 34,403,043
Matches: 24,108,865 out of 34,403,043
Mismatches: 6,121,750 out of 34,403,043
Insertions: 736,643 out of 34,403,043
Identity over aligned base-pairs: 77.9%

Sorghum bicolor

Uncovered: 632,655,992 out of 708,735,318
Covered: 76,079,326 out of 708,735,318

Uncovered: 4,387,848 out of 39,785,927
Matches: 27,471,932 out of 39,785,927
Mismatches: 6,961,972 out of 39,785,927
Insertions: 964,175 out of 39,785,927
Identity over aligned base-pairs: 77.6%

Block size distribution

Size range All 187,234 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,621
9.0 kb
10 bp - 100 bp
26,726
1.7 Mb
9,852
692.0 kb
100 bp - 1 kb
130,787
49.7 Mb
44,546
14.9 Mb
1 kb - 10 kb
28,092
48.4 Mb
13,275
31.2 Mb
10 kb - 100 kb
8
85.1 kb
303
6.1 Mb
100 kb - 1 Mb
17
8.5 Mb
1 Mb - 10 Mb
12
38.5 Mb