Finally, in 2018, a complete black bear genome was sequenced and submitted to GenBank as accession ASM334442v1 in the “Assembly” database. I had been checking regularly with NCBI to see whether a black bear whole genome had been submitted. I was thrilled. It would now be possible to query the Sample 26 sequence against this massive genome of 2.5 billion bases, in 231,673 contigs and 111,495 scaffolds.
The top six hits by score were (Table 1):
Table 1. Sample 26 vs. Black Bear Whole Genome
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Accession#
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%ID
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Length
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Score
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LZNR01001132.1
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100
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1237
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2285
|
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LZNR01003708.1
|
100
|
1157
|
2137
|
|
LZNR01005486.1
|
100
|
1114
|
2058
|
|
LZNR01000516.1
|
100
|
1103
|
2037
|
|
LZNR01074398.1
|
100
|
1093
|
2019
|
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LZNR01003247.1
|
100
|
1043
|
1927
|
Table 1. #These are scaffolds.
Fig. 1 shows the plot of all hits above 99.5%ID and 200 bp. As mentioned above, the solid line at 100%ID contains 1725 hits. There are 849 other hits above 99.5%ID in this figure.
Figure 1. Each diamond represents a hit > 200bp and 99.5%ID. Abscissa is hit starting point on Sample 26 sequence. Most of the data are in the 100%ID solid line of overlapping points.
And Melba, bears have mutations too, so 100%ID is not required for a species match. Depending on the phylogeny, above 99-99.5% is considered a good species match. The whole system of human haplogroups is based on mutations and slight mismatches of mtDNA. We don't always match each other 100% either.
And Melba, bears have mutations too, so 100%ID is not required for a species match. Depending on the phylogeny, above 99-99.5% is considered a good species match. The whole system of human haplogroups is based on mutations and slight mismatches of mtDNA. We don't always match each other 100% either.