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Arabidopsis thaliana vs Actinidia chinensis LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) 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. Arabidopsis thaliana 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

ParameterArabidopsis thalianaActinidia chinensis
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 105,806 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 85,327,221 out of 119,667,750
Covered: 34,340,529 out of 119,667,750

Uncovered: 8,681,592 out of 33,775,569
Matches: 16,982,403 out of 33,775,569
Mismatches: 7,575,974 out of 33,775,569
Insertions: 535,600 out of 33,775,569
Identity over aligned base-pairs: 67.7%

Actinidia chinensis

Uncovered: 526,138,457 out of 553,842,477
Covered: 27,704,020 out of 553,842,477

Uncovered: 24,240,912 out of 42,227,027
Matches: 12,229,284 out of 42,227,027
Mismatches: 5,285,145 out of 42,227,027
Insertions: 471,686 out of 42,227,027
Identity over aligned base-pairs: 68.0%

Block size distribution

Size range All 105,806 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,127
5.6 kb
10 bp - 100 bp
16,385
1.1 Mb
3,947
277.3 kb
100 bp - 1 kb
82,329
26.7 Mb
17,533
6.6 Mb
1 kb - 10 kb
5,964
9.1 Mb
11,049
26.9 Mb
10 kb - 100 kb
1
12.3 kb
214
3.1 Mb