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Arabidopsis thaliana vs Chenopodium quinoa LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Chenopodium quinoa (Chenopodium quinoa, ASM168347v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 103. 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 thalianaChenopodium quinoa
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 187,647 alignment blocks

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

Uncovered: 88,875,168 out of 119,667,750
Covered: 30,792,582 out of 119,667,750

Uncovered: 12,007,859 out of 33,775,569
Matches: 14,513,778 out of 33,775,569
Mismatches: 6,763,995 out of 33,775,569
Insertions: 489,937 out of 33,775,569
Identity over aligned base-pairs: 66.7%

Chenopodium quinoa

Uncovered: 1,277,925,925 out of 1,333,398,936
Covered: 55,473,011 out of 1,333,398,936

Uncovered: 18,297,680 out of 43,819,804
Matches: 16,993,923 out of 43,819,804
Mismatches: 7,897,444 out of 43,819,804
Insertions: 630,757 out of 43,819,804
Identity over aligned base-pairs: 66.6%

Block size distribution

Size range All 187,647 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,440
7.8 kb
10 bp - 100 bp
27,722
1.9 Mb
6,950
493.2 kb
100 bp - 1 kb
147,348
49.4 Mb
38,602
15.2 Mb
1 kb - 10 kb
11,135
16.5 Mb
22,571
49.9 Mb
10 kb - 100 kb
2
53.7 kb
167
2.3 Mb