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Triticum aestivum vs Triticum aestivum Kariega LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Kariega (Triticum aestivum, Tae_Kariega_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 113. Triticum aestivum 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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

ParameterTriticum aestivumTriticum aestivum Kariega
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,362,911 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 1,980,549,530 out of 14,547,261,565
Covered: 12,566,712,035 out of 14,547,261,565

Uncovered: 3,538,690 out of 133,674,966
Matches: 129,200,655 out of 133,674,966
Mismatches: 835,470 out of 133,674,966
Insertions: 100,151 out of 133,674,966
Identity over aligned base-pairs: 99.3%

Triticum aestivum Kariega

Uncovered: 2,015,910,499 out of 14,677,204,660
Covered: 12,661,294,161 out of 14,677,204,660

Uncovered: 18,180,804 out of 169,895,682
Matches: 150,250,845 out of 169,895,682
Mismatches: 1,369,306 out of 169,895,682
Insertions: 94,727 out of 169,895,682
Identity over aligned base-pairs: 99.0%

Block size distribution

Size range All 1,362,911 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13,590
81.6 kb
10 bp - 100 bp
218,494
11.8 Mb
91,347
5.4 Mb
100 bp - 1 kb
475,630
178.5 Mb
225,260
80.0 Mb
1 kb - 10 kb
346,198
1.4 Gb
98,274
290.2 Mb
10 kb - 100 kb
295,220
9.5 Gb
6,636
126.0 Mb
100 kb - 1 Mb
13,779
1.8 Gb
385
142.4 Mb
1 Mb - 10 Mb
96
344.9 Mb
10 Mb - 100 Mb
21
413.6 Mb
100 Mb - 1 Gb
21
11.6 Gb