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Oryza sativa Japonica Group vs Actinidia chinensis LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Actinidia chinensis (Actinidia chinensis var. chinensis, Red5_PS1_1.69.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 96. 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 GroupActinidia chinensis
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 110,167 alignment blocks

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

Uncovered: 341,375,015 out of 375,049,285
Covered: 33,674,270 out of 375,049,285

Uncovered: 13,652,115 out of 34,818,902
Matches: 13,854,543 out of 34,818,902
Mismatches: 6,802,690 out of 34,818,902
Insertions: 509,554 out of 34,818,902
Identity over aligned base-pairs: 65.5%

Actinidia chinensis

Uncovered: 530,670,961 out of 553,842,477
Covered: 23,171,516 out of 553,842,477

Uncovered: 26,838,940 out of 42,227,027
Matches: 10,197,925 out of 42,227,027
Mismatches: 4,852,217 out of 42,227,027
Insertions: 337,945 out of 42,227,027
Identity over aligned base-pairs: 66.3%

Block size distribution

Size range All 110,167 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,003
4.8 kb
10 bp - 100 bp
18,236
1.3 Mb
4,677
332.7 kb
100 bp - 1 kb
85,946
26.5 Mb
25,686
9.7 Mb
1 kb - 10 kb
4,982
7.8 Mb
12,139
25.3 Mb
10 kb - 100 kb
26
319.2 kb