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Oryza sativa Japonica Group vs Corchorus capsularis LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Corchorus capsularis (Corchorus capsularis, CCACVL1_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 GroupCorchorus capsularis
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 123,809 alignment blocks

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

Uncovered: 342,838,883 out of 375,049,285
Covered: 32,210,402 out of 375,049,285

Uncovered: 14,912,988 out of 34,818,902
Matches: 12,922,867 out of 34,818,902
Mismatches: 6,533,721 out of 34,818,902
Insertions: 449,326 out of 34,818,902
Identity over aligned base-pairs: 64.9%

Corchorus capsularis

Uncovered: 288,516,233 out of 317,178,409
Covered: 28,662,176 out of 317,178,409

Uncovered: 13,040,705 out of 30,371,305
Matches: 11,353,888 out of 30,371,305
Mismatches: 5,607,786 out of 30,371,305
Insertions: 368,926 out of 30,371,305
Identity over aligned base-pairs: 65.5%

Block size distribution

Size range All 123,809 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
887
4.6 kb
10 bp - 100 bp
18,886
1.3 Mb
3,561
259.9 kb
100 bp - 1 kb
96,554
31.9 Mb
25,397
10.4 Mb
1 kb - 10 kb
7,481
10.9 Mb
15,595
33.0 Mb
10 kb - 100 kb
1
10.2 kb
38
472.3 kb