In this section

Bigelowiella natans vs Guillardia theta CCMP2712 LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Bigelowiella natans 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

ParameterBigelowiella natansGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,809 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Bigelowiella natans

Uncovered: 93,381,962 out of 94,701,163
Covered: 1,319,201 out of 94,701,163

Uncovered: 27,637,705 out of 28,817,508
Matches: 739,839 out of 28,817,508
Mismatches: 403,527 out of 28,817,508
Insertions: 36,437 out of 28,817,508
Identity over aligned base-pairs: 62.7%

Guillardia theta CCMP2712

Uncovered: 85,778,662 out of 87,266,873
Covered: 1,488,211 out of 87,266,873

Uncovered: 29,309,797 out of 30,644,092
Matches: 823,814 out of 30,644,092
Mismatches: 463,345 out of 30,644,092
Insertions: 47,136 out of 30,644,092
Identity over aligned base-pairs: 61.7%

Block size distribution

Size range All 7,809 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
47
249.0 bp
10 bp - 100 bp
3,074
209.5 kb
688
48.1 kb
100 bp - 1 kb
4,393
1.2 Mb
2,248
844.4 kb
1 kb - 10 kb
295
495.4 kb
465
916.8 kb
10 kb - 100 kb
6
68.8 kb