1##fileformat=VCFv4.2 2##ALT=<ID=CPX,Description="Complex rearrangement of reference sequence"> 3##ALT=<ID=DEL,Description="Deletion relative to the reference"> 4##ALT=<ID=DUP,Description="Region of elevated copy number relative to the reference"> 5##ALT=<ID=DUP:INV,Description="Region of elevated copy number relative to the reference, with some copies inverted"> 6##ALT=<ID=INS,Description="Insertion of novel sequence relative to the reference"> 7##ALT=<ID=INV,Description="Inversion of reference sequence"> 8##INFO=<ID=ALIGN_LENGTHS,Number=.,Type=Integer,Description="Minimum lengths of the flanking aligned region from each contig alignment"> 9##INFO=<ID=ALT_ARRANGEMENT,Number=.,Type=String,Description="For CPX variants only; specifies how reference segments given in SEGMENTS are re-arranged"> 10##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> 11##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> 12##INFO=<ID=CONTRACTION,Number=0,Type=Flag,Description="Tandem repeats contraction compared to reference"> 13##INFO=<ID=CPX_EVENT,Number=.,Type=String,Description="ID(s) of CPX event(s) from which current simple variant record is extracted"> 14##INFO=<ID=CTG_GOOD_NONCANONICAL_MAPPING,Number=.,Type=String,Description="Good mapping of evidence contigs as listed in CTG_NAMES to non-canonical reference chromosomes that could potentially offer better explanation of the assembly contig without the SV record. One for each evidence assembly contig, if available; otherwise a \".\". If no evidence contig has such mapping, this annotation is omitted for the record."> 15##INFO=<ID=CTG_NAMES,Number=.,Type=String,Description="Name of local assembly contigs supporting this variant, formatted as \"asm%06d:tig%05d\""> 16##INFO=<ID=DUP_ANNOTATIONS_IMPRECISE,Number=0,Type=Flag,Description="Whether the duplication annotations are from an experimental optimization procedure"> 17##INFO=<ID=DUP_IMPRECISE_AFFECTED_RANGE,Number=.,Type=String,Description="Affected reference range for duplications annotated with the flag DUP_ANNOTATIONS_IMPRECISE"> 18##INFO=<ID=DUP_NUM,Number=R,Type=Integer,Description="Number of times the sequence is duplicated on reference and on the alternate alleles"> 19##INFO=<ID=DUP_ORIENTATIONS,Number=A,Type=String,Description="Orientations of the duplicated sequence on alt allele relative to the copy on ref; one group for each alt allele (currently only available for inverted duplication variants)"> 20##INFO=<ID=DUP_REPEAT_UNIT_REF_SPAN,Number=1,Type=String,Description="Reference span of the suspected repeated unit in a tandem duplication"> 21##INFO=<ID=DUP_SEQ_CIGARS,Number=.,Type=String,Description="CIGARs of the repeated sequence on the locally-assembled contigs when aligned to DUP_REPEAT_UNIT_REF_SPAN (currently only available for repeats when DUP_ANNOTATIONS_IMPRECISE is false)"> 22##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> 23##INFO=<ID=EXPANSION,Number=0,Type=Flag,Description="Tandem repeats expansion compared to reference"> 24##INFO=<ID=EXTERNAL_CNV_CALLS,Number=1,Type=String,Description="Comma-delimited list of external copy number calls that overlap with this variant in format ID:CN:CNQ"> 25##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints"> 26##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints"> 27##INFO=<ID=HQ_MAPPINGS,Number=1,Type=Integer,Description="Number of high-quality contig alignments that support the variant"> 28##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> 29##INFO=<ID=INSLEN,Number=A,Type=Integer,Description="Length of inserted sequence (note for duplication records, this does not count the extra copies of the duplicated sequence)"> 30##INFO=<ID=INSSEQ,Number=.,Type=String,Description="Inserted sequence at the breakpoint"> 31##INFO=<ID=INSSEQ_MAP,Number=.,Type=String,Description="Alignments of inserted sequence"> 32##INFO=<ID=INV33,Number=0,Type=Flag,Description="Whether the event represents a 3' to 5' breakpoint"> 33##INFO=<ID=INV55,Number=0,Type=Flag,Description="Whether the event represents a 5' to 3' breakpoint"> 34##INFO=<ID=LINK,Number=.,Type=String,Description="ID(s) of other variants that are linked to this record, i.e. they constitute a larger more complex variant"> 35##INFO=<ID=MAPPING_QUALITIES,Number=.,Type=Integer,Description="Mapping qualities of the contig alignments that support the variant"> 36##INFO=<ID=MATEID,Number=.,Type=String,Description="ID(s) for mate(s) of a BND record"> 37##INFO=<ID=MAX_ALIGN_LENGTH,Number=1,Type=Integer,Description="Maximum of the values listed in ALIGN_LENGTHS"> 38##INFO=<ID=READ_PAIR_SUPPORT,Number=1,Type=Integer,Description="Number of discordant read pairs supporting the variant"> 39##INFO=<ID=SEGMENTS,Number=.,Type=String,Description="For CPX variants only; segments of reference that are rearranged"> 40##INFO=<ID=SEQ_ALT_HAPLOTYPE,Number=A,Type=Character,Description="Alt haplotype sequence, one per alt allele"> 41##INFO=<ID=SPLIT_READ_SUPPORT,Number=1,Type=Integer,Description="Number of split read supplementary mappings supporting the variant"> 42##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> 43##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> 44##INFO=<ID=TOTAL_MAPPINGS,Number=1,Type=Integer,Description="Number of local assembly contigs supporting the variant, i.e. number of entries in CTG_NAMES"> 45##FILTER=<ID=LOW_MQ,Description="Assembly evidence based record that whose maximum value specified in MAPPING_QUALITIES is lower than user specified threshold"> 46##FILTER=<ID=SHORT_ALN,Description="Assembly evidence based record that whose MAX_ALIGN_LENGTH value is lower than user specified threshold"> 47##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events"> 48##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events"> 49##contig=<ID=chr20,length=64444167,assembly=38> 50##contig=<ID=chr21,length=46709983,assembly=38> 51#CHROM POS ID REF ALT QUAL FILTER INFO 52chr20 2379968 INS_chr20_2379968_2379968_CPX_DERIVED G <INS> . . CPX_EVENT=CPX_chr20:2379056-2379968;CTG_NAMES=asm027854:tig00003;END=2379968;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1401;SVLEN=213;SVTYPE=INS 53chr20 23122666 DEL_chr20_23122666_23122995_CPX_DERIVED C <DEL> . . ALIGN_LENGTHS=876,876;CPX_EVENT=CPX_chr20:23122561-23122996;CTG_NAMES=asm028059:tig00000,asm028059:tig00001;END=23122995;HQ_MAPPINGS=2;INSLEN=36;INSSEQ=TTCACCTGCAAGCCCTCCCACACGGTGACATGACAG;INSSEQ_MAP=1254_1295_chr20:23122559-23122600_-_1253H42M874H_60_0_42_O,1254_1295_chr20:23122559-23122600_-_1253H42M874H_60_0_42_O;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=876;SEQ_ALT_HAPLOTYPE=TTCACCTGCAAGCCCTCCCACACGGTGACATGACAG;SVLEN=-329;SVTYPE=DEL;TOTAL_MAPPINGS=2 54chr20 38124003 INS-DUPLICATION-TANDEM-EXPANSION_chr20_38124004_38124014_CPX_DERIVED C <INS> . . ALIGN_LENGTHS=231,231;CPX_EVENT=CPX_chr20:38123803-38124181,CPX_chr20:38123803-38124181;CTG_NAMES=asm028411:tig00000,asm028411:tig00001;DUP_NUM=1,2;DUP_ORIENTATIONS=++;DUP_REPEAT_UNIT_REF_SPAN=chr20:38124004-38124014;DUP_SEQ_CIGARS=11M,11M;END=38124003;EXPANSION;HQ_MAPPINGS=2;INSLEN=606;INSSEQ=TAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATATATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAATACACATTATA;INSSEQ_MAP=1523_1590_chr20:38123803-38123868_+_1522H31M2I35M2301H_60_3_43_O,1523_1590_chr20:38123803-38123868_+_1522H31M2I35M2301H_60_3_43_O;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=231;SEQ_ALT_HAPLOTYPE=TATTATATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATATATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATA;SVLEN=617;SVTYPE=INS;TOTAL_MAPPINGS=2 55chr20 38653053 INS_chr20_38653053_38653053_CPX_DERIVED A <INS> . . CPX_EVENT=CPX_chr20:38653054-38653283;CTG_NAMES=asm028418:tig00000;END=38653053;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1534;SVLEN=259;SVTYPE=INS 56chr20 38653112 INS-DUPLICATION-TANDEM-EXPANSION_chr20_38653113_38653268_CPX_DERIVED A <DUP> . . ALIGN_LENGTHS=224;CPX_EVENT=CPX_chr20:38653054-38653283;CTG_NAMES=asm028418:tig00000;DUP_NUM=1,2;DUP_ORIENTATIONS=++;DUP_REPEAT_UNIT_REF_SPAN=chr20:38653113-38653268;DUP_SEQ_CIGARS=67M44I89M,57M21I99M;END=38653112;EXPANSION;HQ_MAPPINGS=1;INSLEN=135;INSSEQ=CTGGTGATGATAATGGTGGTGGTGGTGGTGATGGTGATGATGATTATGATGGTGGTGGTGGTGGTGGTGGTGCTGGTGATAGTGGTGGTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGATGATGGTGATG;INSSEQ_MAP=1546_1871_chr20:38653054-38653385_-_1545H128M15D64M6I105M3I20M1613H_59_53_100_O;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=224;SEQ_ALT_HAPLOTYPE=ATGATTGTGATGGTGGTGTTGGTGGTGGTGATAATGATGGTAGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGGTGATGGAAATGATGATGATGTTAATTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGATGGTGATGATGATTATGATGGTGGTGGTGGTGGTGGTGGTGCTGGTGATAGTGGTGGTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGGTGTTGGTGGTGCTGGTGATGATAATCATGCTGGTGGTGGTGGCGTTGATGATGGTGACAGTAGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGATGGTGGTGGTGGTG;SVLEN=291;SVTYPE=DUP;TOTAL_MAPPINGS=1 57chr20 38653283 INS_chr20_38653283_38653283_CPX_DERIVED G <INS> . . CPX_EVENT=CPX_chr20:38653054-38653283;CTG_NAMES=asm028418:tig00000;END=38653283;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1534;SVLEN=175;SVTYPE=INS 58chr20 47895195 DEL_chr20_47895195_47895293_CPX_DERIVED A <DEL> . . CPX_EVENT=CPX_chr20:47895195-47895581;CTG_NAMES=asm028508:tig00005;END=47895293;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=289;SVLEN=-98;SVTYPE=DEL 59chr20 47895482 DEL_chr20_47895482_47895580_CPX_DERIVED G <DEL> . . ALIGN_LENGTHS=189;CPX_EVENT=CPX_chr20:47895195-47895581;CTG_NAMES=asm028508:tig00005;END=47895580;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=189;SVLEN=-98;SVTYPE=DEL;TOTAL_MAPPINGS=1 60chr20 61375462 INS-DUPLICATION-TANDEM-EXPANSION_chr20_61375463_61375819_CPX_DERIVED A <DUP> . . ALIGN_LENGTHS=358;CPX_EVENT=CPX_chr20:61375650-61376102;CTG_NAMES=asm028687:tig00001;DUP_ANNOTATIONS_IMPRECISE;DUP_IMPRECISE_AFFECTED_RANGE=chr20:61375463-61376102;DUP_NUM=1,2;DUP_ORIENTATIONS=++;DUP_REPEAT_UNIT_REF_SPAN=chr20:61375463-61375819;END=61375462;EXPANSION;HOMLEN=283;HOMSEQ=GTGATGGTGTGGTTTGTTGATGGTAGTGTGATGCTCTTGGTGCTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGATGATAGTGGGGTTTATTGATGGTAGTGTGATGGTCTTGGTGGTGCTGATAATGGTGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTGG;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=358;SEQ_ALT_HAPLOTYPE=GTGATGGTGTGGTTTATTGATGGCAGTGTGATTGTCTTGGTGGTGGTGATGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGATGGTGGCGCTGGTGGTGGTCATAGCACTGGTGGTGGTCATAGCACTGGTGGTGATGGTATGGTTTGTTGATGGTAGTGTGATGATCTTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTAGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGCTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGCTCTTGGTGCTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGATGATAGTGGGGTTTATTGATGGTAGTGTGATGGTCTTGGTGGTGCTGATAATGGTGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTGGCGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGGTGGTGATGATGTAGTTTGTTGATGGTAGCGTGATGTTCTTGGTGCTGGTGGTGGTGATGATGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGGTGGTGGTGATAGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGATGCTGGTGATGGTATTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTCGTGGTGGTGGTGTGGTTTGTCGATGGTAGTGTGGTGGTCTTGGTGCTGGTGG;SVLEN=357;SVTYPE=DUP;TOTAL_MAPPINGS=1 61chr20 61375649 INS-DUPLICATION-TANDEM-EXPANSION_chr20_61375650_61375892_CPX_DERIVED T <DUP> . . ALIGN_LENGTHS=430;CPX_EVENT=CPX_chr20:61375650-61376102;CTG_NAMES=asm028687:tig00001;DUP_ANNOTATIONS_IMPRECISE;DUP_IMPRECISE_AFFECTED_RANGE=chr20:61375650-61376103;DUP_NUM=1,2;DUP_ORIENTATIONS=++;DUP_REPEAT_UNIT_REF_SPAN=chr20:61375650-61375892;END=61375649;EXPANSION;HOMLEN=211;HOMSEQ=TGGTGGTGGTGATGATGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGGTGGTGGTGATAGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGATGCTGGTGATGGTATTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTCGTGGTGGTGGTGTGGTTTGTCGATGGTAGTGTGGTGGTCTTGGTGCTGGTGGT;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=430;SEQ_ALT_HAPLOTYPE=TGGTGGTGATGATAGTGGGGTTTATTGATGGTAGTGTGATGGTCTTGGTGGTGCTGATAATGGTGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTGGCGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGGTGGTGATGATGTAGTTTGTTGATGGTAGCGTGATGTTCTTGGTGCTGGTGGTGGTGATGATGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGGTGGTGGTGATAGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGATGCTGGTGATGGTATTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTCGTGGTGGTGGTGTGGTTTGTCGATGGTAGTGTGGTGGTCTTGGTGCTGGTGGTTGTCGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGGTGATGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTAGTGATGGTGTGGTTTGCTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATACTGTGGTTTGTGGATGGTAGTGTGATGGTCTTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGT;SVLEN=243;SVTYPE=DUP;TOTAL_MAPPINGS=1 62chr20 61375649 INS_chr20_61375649_61375649_CPX_DERIVED T <INS> . . CPX_EVENT=CPX_chr20:61375650-61376102;CTG_NAMES=asm028687:tig00001;END=61375649;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1559;SVLEN=572;SVTYPE=INS 63chr20 61919907 INS-DUPLICATION-TANDEM-EXPANSION_chr20_61919908_61920054_CPX_DERIVED C <DUP> . . ALIGN_LENGTHS=149;CPX_EVENT=CPX_chr20:61919906-61920109;CTG_NAMES=asm028707:tig00000;DUP_ANNOTATIONS_IMPRECISE;DUP_IMPRECISE_AFFECTED_RANGE=chr20:61919908-61920109;DUP_NUM=1,2;DUP_ORIENTATIONS=++;DUP_REPEAT_UNIT_REF_SPAN=chr20:61919908-61920054;END=61919907;EXPANSION;HOMLEN=55;HOMSEQ=GTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTG;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=149;SEQ_ALT_HAPLOTYPE=GTGATTGTGTGGAAGTGTGATGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGGAAGTGTGGTGTCACGCTGATTGCATGGAAGTGTGTTGTGATTGTGTGGAAGCGTGATATCGCAGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATCGGAAGCGTGGTGTTGCGGTGATTGCATGGAAGCATGTTGTGATTGTGTGGAAGCATGGTATCGTGATTGTCTGGAAGCATGGTGTCATGGTGATTGGAAGTGTGTCGTGATTG;SVLEN=147;SVTYPE=DUP;TOTAL_MAPPINGS=1 64chr20 61920109 INS_chr20_61920109_61920109_CPX_DERIVED G <INS> . . CPX_EVENT=CPX_chr20:61919906-61920109;CTG_NAMES=asm028707:tig00000;END=61920109;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=947;SVLEN=531;SVTYPE=INS 65chr20 62452037 INS-DUPLICATION-TANDEM-EXPANSION_chr20_62452038_62452041_CPX_DERIVED A <INS> . . ALIGN_LENGTHS=59;CPX_EVENT=CPX_chr20:62452038-62452236;CTG_NAMES=asm028732:tig00001;DUP_NUM=1,2;DUP_ORIENTATIONS=++;DUP_REPEAT_UNIT_REF_SPAN=chr20:62452038-62452041;DUP_SEQ_CIGARS=4M,4M;END=62452037;EXPANSION;HQ_MAPPINGS=1;INSLEN=149;INSSEQ=GGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGAGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=59;SEQ_ALT_HAPLOTYPE=GGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGAGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG;SVLEN=153;SVTYPE=INS;TOTAL_MAPPINGS=1 66chr20 62452087 DEL_chr20_62452087_62452235_CPX_DERIVED A <DEL> . . ALIGN_LENGTHS=50;CPX_EVENT=CPX_chr20:62452038-62452236;CTG_NAMES=asm028732:tig00001;END=62452235;HOMLEN=9;HOMSEQ=GAAGGAGAG;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=50;SVLEN=-148;SVTYPE=DEL;TOTAL_MAPPINGS=1 67chr20 63092255 INS_chr20_63092255_63092255_CPX_DERIVED G <INS> . . ALIGN_LENGTHS=1091;CPX_EVENT=CPX_chr20:63092255-63094246;CTG_NAMES=asm028762:tig00002;END=63092255;HQ_MAPPINGS=1;INSLEN=71;INSSEQ=GCCCAGGTTCCCGGGGCTGCGTGGGAGACACAGAAGTGGGGGCACCTCCGCAGCACCCACATCCTGCCGAT;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1091;SEQ_ALT_HAPLOTYPE=GCCCAGGTTCCCGGGGCTGCGTGGGAGACACAGAAGTGGGGGCACCTCCGCAGCACCCACATCCTGCCGAT;SVLEN=71;SVTYPE=INS;TOTAL_MAPPINGS=1 68chr20 63093346 DEL_chr20_63093346_63094245_CPX_DERIVED G <DEL> . . ALIGN_LENGTHS=942;CPX_EVENT=CPX_chr20:63092255-63094246;CTG_NAMES=asm028762:tig00002;END=63094245;HQ_MAPPINGS=1;INSLEN=1;INSSEQ=T;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=942;SEQ_ALT_HAPLOTYPE=T;SVLEN=-899;SVTYPE=DEL;TOTAL_MAPPINGS=1 69chr20 63353949 DEL_chr20_63353949_63354001_CPX_DERIVED T <DEL> . . ALIGN_LENGTHS=80;CPX_EVENT=CPX_chr20:63353949-63354272;CTG_NAMES=asm028777:tig00001;END=63354001;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=80;SVLEN=-52;SVTYPE=DEL;TOTAL_MAPPINGS=1 70chr20 63354205 DEL_chr20_63354205_63354271_CPX_DERIVED G <DEL> . . CPX_EVENT=CPX_chr20:63353949-63354272;CTG_NAMES=asm028777:tig00001;END=63354271;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=81;SVLEN=-66;SVTYPE=DEL 71chr21 21264943 INS_chr21_21264943_21264943_CPX_DERIVED G <INS> . . CPX_EVENT=CPX_chr21:21264944-21265096;CTG_NAMES=asm029034:tig00000,asm029034:tig00001;END=21264943;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=316;SVLEN=221;SVTYPE=INS 72chr21 21264961 INS-DUPLICATION-TANDEM-EXPANSION_chr21_21264962_21265070_CPX_DERIVED G <DUP> . . ALIGN_LENGTHS=110,110;CPX_EVENT=CPX_chr21:21264944-21265096,CPX_chr21:21264944-21265096;CTG_NAMES=asm029034:tig00000,asm029034:tig00001;DUP_ANNOTATIONS_IMPRECISE;DUP_IMPRECISE_AFFECTED_RANGE=chr21:21264962-21265096;DUP_NUM=1,2;DUP_ORIENTATIONS=++;DUP_REPEAT_UNIT_REF_SPAN=chr21:21264962-21265070;END=21264961;EXPANSION;HOMLEN=26;HOMSEQ=TATATATACACATATATATTATATAT;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=110;SEQ_ALT_HAPLOTYPE=TATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATATGTATATATACACATATATATTATATATATATGTGTCTGTATATATATACACATATATATTATATAT;SVLEN=109;SVTYPE=DUP;TOTAL_MAPPINGS=2 73chr21 23428920 INS_chr21_23428920_23428920_CPX_DERIVED T <INS> . . CPX_EVENT=CPX_chr21:23428920-23429023;CTG_NAMES=asm029052:tig00000,asm029052:tig00001;END=23428920;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1182;SVLEN=85;SVTYPE=INS 74chr21 23428920 INS_chr21_23428920_23428967_CPX_DERIVED TTTATATAAATATATATAAATATATAATATATAATAATATAATATAAT <INS> . . ALIGN_LENGTHS=56,56;CPX_EVENT=CPX_chr21:23428920-23429023,CPX_chr21:23428920-23429023;CTG_NAMES=asm029052:tig00000,asm029052:tig00001;END=23428967;HQ_MAPPINGS=2;INSLEN=85;INSSEQ=ATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATA;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=56;SEQ_ALT_HAPLOTYPE=ATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATA;SVLEN=85;SVTYPE=INS;TOTAL_MAPPINGS=2 75chr21 26001843 INV_chr21_26001843_26002384_CPX_DERIVED T <INV> . . CPX_EVENT=CPX_chr21:26001843-26002386;CTG_NAMES=asm029075:tig00000;END=26002384;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1370;SVLEN=0;SVTYPE=INV 76chr21 46069065 INS_chr21_46069065_46069065_CPX_DERIVED C <INS> . . ALIGN_LENGTHS=91,91;CPX_EVENT=CPX_chr21:46069065-46069209;CTG_NAMES=asm029362:tig00001,asm029362:tig00002;END=46069065;HQ_MAPPINGS=2;INSLEN=60;INSSEQ=CTAGGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGCACACGTGTGT;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=91;SEQ_ALT_HAPLOTYPE=CTAGGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGCACACGTGTGT;SVLEN=60;SVTYPE=INS;TOTAL_MAPPINGS=2 77chr21 46069156 DEL_chr21_46069156_46069208_CPX_DERIVED A <DEL> . . ALIGN_LENGTHS=91,91;CPX_EVENT=CPX_chr21:46069065-46069209;CTG_NAMES=asm029362:tig00001,asm029362:tig00002;END=46069208;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=91;SVLEN=-52;SVTYPE=DEL;TOTAL_MAPPINGS=2 78