Table 1 SNV and indel variant-calling statistics of the prostate cancer cell lines PC3 and LNCaP
PC3 PrivateLNCaP PrivateShared
Number and percentage of variants by type
 SNVs318,38034.0%404,28272.1%166,91265.0%
 Indels618,14966.0%156,18227.9%89,91935.0%
Number of events by type
 3′-UTR15,57210,5003938
 5′-UTR premature start codon21128949
 5′-UTR26131868692
 Conservative_inframe_deletion39227
 Conservative_inframe_insertion46811972
 Disruptive_inframe_deletion62197
 Disruptive_inframe_insertion1726444
 Downstream_gene107,76156,72829,770
 Frameshift27616744
 Intergenic_region563,630326,261175,014
 Intron916,272576,268191,182
 Missense352057171667
 Non_coding_transcript_exon584838462091
 Non_coding_transcript18101
 Protein_protein_contact120175
 Sequence_feature797859301457
 Splice_acceptor8013121
 Splice_donor5613817
 Splice_region13131174437
 Start_lost16143
 Stop_gained5837829
 Stop_lost2549
 Structural_interaction11608081
 Synonymous2402272781
 Upstream_gene107,28157,4471301
  • Common germline variants were excluded and variants were further filtered using SnpSift, with a total depth threshold at 30 (DP ≥ 30) and a minimum variance confidence of 200 (QUAL ≥ 200), and annotated by SnpEff. SNV, single nucleotide variant; UTR, untranslated region.