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Arabidopsis thaliana vs Beta vulgaris LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Beta vulgaris (Beta vulgaris subsp. vulgaris, RefBeet-1.2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 thalianaBeta 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 123,292 alignment blocks

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

Uncovered: 88,600,055 out of 119,667,750
Covered: 31,067,695 out of 119,667,750

Uncovered: 10,807,871 out of 33,775,569
Matches: 15,352,309 out of 33,775,569
Mismatches: 7,142,768 out of 33,775,569
Insertions: 472,621 out of 33,775,569
Identity over aligned base-pairs: 66.8%

Beta vulgaris

Uncovered: 535,031,763 out of 566,181,630
Covered: 31,149,867 out of 566,181,630

Uncovered: 9,535,674 out of 28,257,705
Matches: 12,454,561 out of 28,257,705
Mismatches: 5,792,775 out of 28,257,705
Insertions: 474,695 out of 28,257,705
Identity over aligned base-pairs: 66.5%

Block size distribution

Size range All 123,292 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
772
4.1 kb
10 bp - 100 bp
18,359
1.3 Mb
4,952
353.4 kb
100 bp - 1 kb
97,102
31.9 Mb
27,891
10.8 Mb
1 kb - 10 kb
7,053
10.5 Mb
14,592
31.4 Mb
10 kb - 100 kb
6
92.2 kb
88
1.3 Mb