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Arabidopsis thaliana vs Malus domestica Golden LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Malus domestica Golden (Malus domestica, ASM211411v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 thalianaMalus domestica Golden
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 202,890 alignment blocks

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

Uncovered: 81,366,249 out of 119,667,750
Covered: 38,301,501 out of 119,667,750

Uncovered: 7,730,774 out of 33,775,569
Matches: 17,491,343 out of 33,775,569
Mismatches: 7,973,114 out of 33,775,569
Insertions: 580,338 out of 33,775,569
Identity over aligned base-pairs: 67.2%

Malus domestica Golden

Uncovered: 639,035,198 out of 702,961,352
Covered: 63,926,154 out of 702,961,352

Uncovered: 11,637,042 out of 47,560,911
Matches: 24,234,886 out of 47,560,911
Mismatches: 10,666,193 out of 47,560,911
Insertions: 1,022,790 out of 47,560,911
Identity over aligned base-pairs: 67.5%

Block size distribution

Size range All 202,890 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,098
11.2 kb
10 bp - 100 bp
33,269
2.2 Mb
7,974
585.5 kb
100 bp - 1 kb
151,724
51.9 Mb
43,187
15.5 Mb
1 kb - 10 kb
15,769
24.4 Mb
22,033
53.9 Mb
10 kb - 100 kb
30
648.4 kb
545
9.1 Mb
100 kb - 1 Mb
1
112.5 kb