Whole genome sequence analysis of BT-474 using complete Genomics’ standard and long fragment read technologies

GigaScience

Table 1 BT-474 genome statistics

Metric	BT-474 STD	BT-474 LFR1	BT-474 LFR2
Fully called genome fraction	0.972	0.915	0.900
Fully called exome fraction	0.988	0.928	0.920
Gross mapping yield (Gb)	343	298	261
Both mates mapped yield (Gb)	306	217	171
Genome fraction with sequence coverage ≥ 5x	0.997	0.981	0.978
Exome fraction with sequence coverage ≥ 5x	0.999	0.980	0.980
SNV total count	3,241,932	2,856,624	2,890,506
Homozygous SNV count	1,531,723	1,382,653	1,241,444
Heterozygous SNV count	1,635,402	1,195,290	1,239,735
Het/Hom ratio	1.07	0.86	1.00
ENA sample accession number	ERS823996	ERS823998	ERS823997

STD and LFR libraries were mapped to the NCBI reference genome build 37. An explanation of the genome statistics are as follows: fully called genome fraction, the fraction of the genome for which both alleles at each position are confidently called; fully called exome fraction, the fraction of the coding part of the genome for which both alleles are confidently called; gross mapping yield (Gb), the number of gigabases of read data that can be mapped to NCBI reference genome build 37; both mates mapped yield (Gb), the number of gigabases of read data where both arms of a mate pair can be mapped to NCBI reference genome build 37; genome fraction with sequence coverage ≥ 5x, fraction of the genome with at least 5 reads covering a single position; exome fraction with sequence coverage ≥ 5x, fraction of the coding genome with at least 5 reads covering a single position; SNV total count, the total number of single nucleotide variants called in each library; homozygous SNV count, the total number of homozygous variants called in each library; heterozygous SNV count, the total number of heterozygous variants called in each library; Het/Hom ratio, the ratio of heterozygous variants over homozygous variants (this number is typically around 1.6 for a Caucasian genome); ENA sample accession number, the European Nucleotide Archive accession number to locate the raw read data for each library

ISSN: 2047-217X