1##fileformat=VCFv4.2 2##ALT=<ID=DEL,Description="Deletion relative to the reference"> 3##ALT=<ID=DUP,Description="Region of elevated copy number relative to the reference"> 4##ALT=<ID=DUP:INV,Description="Region of elevated copy number relative to the reference, with some copies inverted"> 5##ALT=<ID=INS,Description="Insertion of novel sequence relative to the reference"> 6##ALT=<ID=INV,Description="Inversion of reference sequence"> 7##INFO=<ID=ALIGN_LENGTHS,Number=.,Type=Integer,Description="Minimum lengths of the flanking aligned region from each contig alignment"> 8##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> 9##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> 10##INFO=<ID=CONTRACTION,Number=0,Type=Flag,Description="Tandem repeats contraction compared to reference"> 11##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."> 12##INFO=<ID=CTG_NAMES,Number=.,Type=String,Description="Name of local assembly contigs supporting this variant, formatted as \"asm%06d:tig%05d\""> 13##INFO=<ID=DUP_ANNOTATIONS_IMPRECISE,Number=0,Type=Flag,Description="Whether the duplication annotations are from an experimental optimization procedure"> 14##INFO=<ID=DUP_IMPRECISE_AFFECTED_RANGE,Number=.,Type=String,Description="Affected reference range for duplications annotated with the flag DUP_ANNOTATIONS_IMPRECISE"> 15##INFO=<ID=DUP_NUM,Number=R,Type=Integer,Description="Number of times the sequence is duplicated on reference and on the alternate alleles"> 16##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)"> 17##INFO=<ID=DUP_REPEAT_UNIT_REF_SPAN,Number=1,Type=String,Description="Reference span of the suspected repeated unit in a tandem duplication"> 18##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)"> 19##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> 20##INFO=<ID=EXPANSION,Number=0,Type=Flag,Description="Tandem repeats expansion compared to reference"> 21##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"> 22##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints"> 23##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints"> 24##INFO=<ID=HQ_MAPPINGS,Number=1,Type=Integer,Description="Number of high-quality contig alignments that support the variant"> 25##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> 26##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)"> 27##INFO=<ID=INSSEQ,Number=.,Type=String,Description="Inserted sequence at the breakpoint"> 28##INFO=<ID=INSSEQ_MAP,Number=.,Type=String,Description="Alignments of inserted sequence"> 29##INFO=<ID=INV33,Number=0,Type=Flag,Description="Whether the event represents a 3' to 5' breakpoint"> 30##INFO=<ID=INV55,Number=0,Type=Flag,Description="Whether the event represents a 5' to 3' breakpoint"> 31##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"> 32##INFO=<ID=MAPPING_QUALITIES,Number=.,Type=Integer,Description="Mapping qualities of the contig alignments that support the variant"> 33##INFO=<ID=MATEID,Number=.,Type=String,Description="ID(s) for mate(s) of a BND record"> 34##INFO=<ID=MAX_ALIGN_LENGTH,Number=1,Type=Integer,Description="Maximum of the values listed in ALIGN_LENGTHS"> 35##INFO=<ID=READ_PAIR_SUPPORT,Number=1,Type=Integer,Description="Number of discordant read pairs supporting the variant"> 36##INFO=<ID=SEQ_ALT_HAPLOTYPE,Number=A,Type=Character,Description="Alt haplotype sequence, one per alt allele"> 37##INFO=<ID=SPLIT_READ_SUPPORT,Number=1,Type=Integer,Description="Number of split read supplementary mappings supporting the variant"> 38##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> 39##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> 40##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"> 41##contig=<ID=chr20,length=64444167,assembly=38> 42##contig=<ID=chr21,length=46709983,assembly=38> 43#CHROM POS ID REF ALT QUAL FILTER INFO 44chr20 2379056 CPX_chr20:2379056-2379968 C <CPX> . . ALIGN_LENGTHS=1401;ALT_ARRANGEMENT=1,2,3,UINS-4,1,3;CTG_NAMES=asm027854:tig00003;END=2379968;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1401;SEGMENTS=chr20:2379056-2379257,chr20:2379257-2379963,chr20:2379963-2379968;SEQ_ALT_HAPLOTYPE=CTGCTGAAGGTCACACAGCCAGTTTGGCCCAGAGATAACAGAACCCAGGACTCTACTGCCAGGCTATGATGCTCACTTCTAAACTGAGTATGGGCCGGGTGCAGTGGCTCTCACTTGGAATCTCGCACTTTGGGAGGCTGAGGTGGGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAACTGTCTCTACTTAAAATACACAAAAAATTAGCCGGGCATGGTGGCACACGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAAGTAGAGGTTGCACCGAGCTGAGATCGTGCCGCTGCACTTCACCCTAGGTGACAGAGCGAGACCCTGTCTCAAAAAAAAAAAACGAGGAGTATGAATTATTATTTGGGGTCTCGAGCAGTGGGGCAGGCAGTGATTTTGATGCCCTGTCTTCTGGGAGCTCCCGTCCAAGCAAGCCCAGGATGAAAGATAAAAGGGCCCTGAATAAGACCATCATTAGTGGGGAGGAGCCTGACCCTGCATAGGCAGAAAAGCAGCTTCAGCAGGGCCCAGGGTCTACAGGGCAGCAGCCTGCAGGGTGTTGAGGAAGGAGCTGCCCTGGGCTGCTGCCAGATGTCAGTAATTATAAGGCTATGTGGGTCTGCAGACAGCTCATTAAAGACGCTTGATCTGCGTGAAACCAGGAAGCAGAACTCAGCCTCTTTGCCACTTTCTGTAAGAAATCCAACCACATCAAACACTTTGGGGTTTTTATGCAGTTTCCTGAATGTTGGGGTGATCCCAGGGAGCGGCCTCATCCTACTGTGCTCAGCACACGGTTGTCTCCTTACCCTTCCTTGTCTCTTTCCCTCGATTCTACCCCCTCCCACTTCCCCTTCCTCACTGGCCCAGTGAGGCTGCTGAAGGTCACACAGCCAGTTTGGCCCAGAGATAACAGAACCCAGGACTCTACTGCCAGGCTATGATGCTCACTTCTAAACTGAGTATGGGCCGGGTGCAGTGGCTCTCACTTGTAATCTCGCACTTTGGGAGGCTGAGGTGGGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAACTGTGCCCAG;SVLEN=913;SVTYPE=CPX;TOTAL_MAPPINGS=1 45chr20 12558793 CPX_chr20:12558793-12558810 A <CPX> . . ALIGN_LENGTHS=597;ALT_ARRANGEMENT=-chrX:99014092-99014129,UINS-101;CTG_NAMES=asm027960:tig00003;END=12558810;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=597;SEGMENTS=chr20:12558793-12558810;SEQ_ALT_HAPLOTYPE=AGACAAAGAAACAAACAAACAAAACAAAACTATATATATATATATATACACACACACACACACACACACATTATTAAAATTCAGATTTAAATAAACTGACTATAAAAAAGTACTTTTGAAACAAAAACTTTAATCATGATTATATATATTA;SVLEN=18;SVTYPE=CPX;TOTAL_MAPPINGS=1 46chr20 18675721 CPX_chr20:18675721-18675877 T <CPX> . . ALIGN_LENGTHS=564;ALT_ARRANGEMENT=1,UINS-28,1,UINS-64,1;CTG_NAMES=asm028012:tig00004;END=18675877;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=564;SEGMENTS=chr20:18675721-18675877;SEQ_ALT_HAPLOTYPE=TATGTGTATATTTACACACATATATATGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACATATATATGTAAATATACCTATGTGTATGTTTACACATATATATGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATGTAAATATACCTATGTGTATGTTTACACATATATGTGTAAATATACCGATGTGTATGTTTACACATATATGTGTAAATATACCTATGTGTATGTTTACACATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTGTGTTTACACATATATATGTGTAAATATACCTATGTGTGTGTTTACACATATATATGTAAATATACCTATGTGT;SVLEN=157;SVTYPE=CPX;TOTAL_MAPPINGS=1 47chr20 20269131 CPX_chr20:20269131-20269199 A <CPX> . . ALIGN_LENGTHS=40;ALT_ARRANGEMENT=-chrX:137700299-137700331;CTG_NAMES=asm028026:tig00000;END=20269199;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=40;SEGMENTS=chr20:20269131-20269199;SEQ_ALT_HAPLOTYPE=ACACACACACACACACACACACACACACACACACA;SVLEN=69;SVTYPE=CPX;TOTAL_MAPPINGS=1 48chr20 23122561 CPX_chr20:23122561-23122996 C <CPX> . . ALIGN_LENGTHS=876,876;ALT_ARRANGEMENT=1,2,-1;CTG_NAMES=asm028059:tig00000,asm028059:tig00001;END=23122996;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=876;SEGMENTS=chr20:23122561-23122596,chr20:23122596-23122666,chr20:23122666-23122996;SEQ_ALT_HAPLOTYPE=CTGTCATGTCACCGTGTGGGAGGGCTTGCAGGTGAAGTGGTCTGGGAGGGGTCCCCCAGACAAAGCCAAGGTTCTGAGAGTTGGCCCGAACACTGCTGGATTCCACTTCACCTGCAAGCCCTCCCACACGGTGACATGACAGC;SVLEN=436;SVTYPE=CPX;TOTAL_MAPPINGS=2 49chr20 28561412 CPX_chr20:28561412-28561576 A <CPX> . . ALIGN_LENGTHS=416;ALT_ARRANGEMENT=UINS-74,1,UINS-74;CTG_NAMES=asm008294:tig00014;END=28561576;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=416;SEGMENTS=chr20:28561413-28561575;SEQ_ALT_HAPLOTYPE=AACATCATATGTGACAGGCTCTCATAGTCACCATCATCACAGAAATCTCGCGCATGTTACAGAGAAGCACTGTCCTACATCATATGTGACAGGCTCTCATAGTCACCATTCCCATGACCATAGTCATGGGAATCTTGCTCATGTTACAGGGAAGCACTGTCCAACATCATATGTGACAGGCTCTCATCGTCACCATCATCATGGGAATCTTGTGCATGTTACAGGGAAGCATTGTCCTACATCGTATGTGACAGGCTCTCATAATCACTATCATCATGGGAATCCTGTGCATGTTACAGGAAAGAACTGTCCTGC;SVLEN=165;SVTYPE=CPX;TOTAL_MAPPINGS=1 50chr20 38123803 CPX_chr20:38123803-38124181 A <CPX> . . ALIGN_LENGTHS=1516,1516;ALT_ARRANGEMENT=1,2,3,UINS-5,1,UINS-531,3,4,3,4;CTG_NAMES=asm028411:tig00000,asm028411:tig00001;END=38124181;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1516;SEGMENTS=chr20:38123803-38123868,chr20:38123868-38124004,chr20:38124004-38124014,chr20:38124014-38124181;SEQ_ALT_HAPLOTYPE=ATACCTATTATATATAATATACCTATTATATATAAGATACCTATTATATATAATATACATATACCTATTATATATATAATATACCTATTATATATATATAATATACCTATTATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATATAATATACCTATTATATATAATATACCTATTATATATAAAATATACCTATTATATATAATATACCTATTATATACATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATATAATATACCTATTATATGCATTATATAATATATTATATATAATATGCATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATTATATATATAATATACATATTATATGTATTATATATTATATATAATATACATATTATATATTATATATTATATACATATTATATATTATATATTATATACATATTATATATTATATACATATTATATATTATATATTATATACATATTATACATTATATATATCTAAAATATATAATACACATTATATATTATATAATACACATTATATATAATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATATAATACACATTATATATTATATAATACACATTATATATTATATATAATACACATTATATATATAATACACATTATATATTATATATAATACATAATACACATTATATATTATATATAATACACATTATATATAATATATAACACACATTATATATAATATATAACACACATTATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATATATTATATATAATACACATATATTATATATAATACACATTATA;SVLEN=379;SVTYPE=CPX;TOTAL_MAPPINGS=2 51chr20 38653054 CPX_chr20:38653054-38653283 T <CPX> . . ALIGN_LENGTHS=1534;ALT_ARRANGEMENT=1,2,3,4,3,1,2,3,4,5,2,3,4,5;CTG_NAMES=asm028418:tig00000;END=38653283;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1534;SEGMENTS=chr20:38653054-38653113,chr20:38653113-38653145,chr20:38653145-38653179,chr20:38653179-38653273,chr20:38653273-38653283;SEQ_ALT_HAPLOTYPE=TGGTGGTGGTGGTGATGGAAATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGATGGTGGTGGTGGTGGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGGTGATAATGATGGTAGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGGTGATGGAAATGATGATGATGTTAATTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGATGGTGATGATGATTATGATGGTGGTGGTGGTGGTGGTGGTGCTGGTGATAGTGGTGGTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGGTGTTGGTGGTGCTGGTGATGATAATCATGCTGGTGGTGGTGGCGTTGATGATGGTGACAGTAGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGATGGTGGTGGTGGTGGTGATGATGGTGATG;SVLEN=230;SVTYPE=CPX;TOTAL_MAPPINGS=1 52chr20 47895195 CPX_chr20:47895195-47895581 A <CPX> . . ALIGN_LENGTHS=289;ALT_ARRANGEMENT=2;CTG_NAMES=asm028508:tig00005;END=47895581;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=289;SEGMENTS=chr20:47895195-47895294,chr20:47895294-47895482,chr20:47895482-47895581;SEQ_ALT_HAPLOTYPE=AAGGGTCCGGAAGCTGGTGACCCAGGGAGGAGAGGTCTTGATCTGGTCTGAGGGTCGTGGAGCTACAGACCCAGGGAGGAGCAATGTTGTTGTAGTTCGAGGGTCCGGTAGCTGGCAACCCGGGAAAGAGAAGTCTTGTTCGAGTTTGAGGGTCGTGGAGCTGCAGACCCAGGGAGGAGCAATTTTGTTGT;SVLEN=387;SVTYPE=CPX;TOTAL_MAPPINGS=1 53chr20 51740560 CPX_chr20:51740560-51740561 A <CPX> . . ALIGN_LENGTHS=1104,1104;ALT_ARRANGEMENT=-chr18:11642876-11642927,UINS-496;CTG_NAMES=asm028558:tig00002,asm028558:tig00003;END=51740561;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1104;SEQ_ALT_HAPLOTYPE=AATTAGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTAACCAACATGAGGAAACCCCGTCTCTACTAAAAATACAAAATTAGATGGGCGTGGTGGCGCATGCCTGTAATTCAAACTACTTGGAAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGTGGTAAGCCAAGATCATGCCATTGTACTCCAGCATGGGCAACAAGAGTGAGACTCCATCTCAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGTGGGCACCTGTAATCCCAGCTACCCTGGAGACTGAGGCAGAAGAATCGCTTGAACCCAGGAGGCGGAGATTGCAGTGAGCCAAGATTACGCCACTGCACTCCAGCCTGGGCACCAAGAGCAAAACCCTGTCTCAAAAAAATTAACAAATAAAAAGATTTCTGTCTGCCACACGGCTGGTCCATGTGTAAAGACACATTCCTGTTGGTTTTATGTGTCTTGAATTCTAATGGGT;SVLEN=2;SVTYPE=CPX;TOTAL_MAPPINGS=2 54chr20 51740560 CPX_chr20:51740560-51741035 A <CPX> . . ALIGN_LENGTHS=895,895;ALT_ARRANGEMENT=-chr18:11642876-11642927,UINS-496,1,UINS-49;CTG_NAMES=asm028558:tig00000,asm028558:tig00001;END=51741035;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=895;SEGMENTS=chr20:51740561-51741034;SEQ_ALT_HAPLOTYPE=AATTAGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTAACCAACATGAGGAAACCCCGTCTCTACTAAAAATACAAAATTAGATGGGCGTGGTGGCGCATGCCTGTAATTCAAACTACTTGGAAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGTGGTAAGCCAAGATCATGCCATTGTACTCCAGCATGGGCAACAAGAGTGAGACTCCATCTCAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGTGGGCACCTGTAATCCCAGCTACCCTGGAGACTGAGGCAGAAGAATCGCTTGAACCCAGGAGGCGGAGATTGCAGTGAGCCAAGATTACGCCACTGCACTCCAGCCTGGGCACCAAGAGCAAAACCCTGTCTCAAAAAAATTAACAAATAAAAAGATTTCTGTCTGCCACACGGCTGGTCCATGTGTAAAGACACATTCCTGTTGGTTTTATGTGTCTTGAATTCTAATGGGTTTTGTGTTGTTGTTTTTGTTTTTTGAGACAAGGTCTCATTCTGTCACCCAGGCAGGACTGTGGTGGCACCATCATGGCTCAGCGCAGCCTCCTTTTCCCCAGGCTCAAGTGATCCTCTTGCCTCAGCCTCCCACGTGGCTGGGACTACAGGTGTGTACCACCACTCCCGGATAATTTTTTTTATTTTTTATTTTTAGTAAAGACAGTCTCACTATGTTGCCCAGGCTGGTCTCCAACTCCTGGTCTCAAGCAATCCTCCCAGTTCAGCCTCTCAAAGTGCTGGGATTACAGATGTGAGCCACAATACCCGGCCCCAATTCTAATGTTTAAAGAGTACAGTCTACACCTTAAAGCCTGCATTTTATCATCCTGTCCTCACTGCTCTGACTTCTTTACAGTTGTGCTGTCCACCTTGGCGGCTTCTACCACATGTGGCTATTTTAAGTTTCAATTAATTAAAATTAAATTTTAATTTAATTAATTAAAAATAAATTTTAATTAATTAATTAAAAATAAATTTTAAT;SVLEN=476;SVTYPE=CPX;TOTAL_MAPPINGS=2 55chr20 54849491 CPX_chr20:54849491-54849615 C <CPX> . . ALIGN_LENGTHS=88;ALT_ARRANGEMENT=UINS-36,-chr14:58474127-58474172,UINS-54;CTG_NAMES=asm028586:tig00000;END=54849615;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=88;SEGMENTS=chr20:54849491-54849615;SEQ_ALT_HAPLOTYPE=CCAAATCTCATGTTGAAATGTAATCCCCAGTGTTGGAGGGGGGCAGATCCCTCATGAATGGCTTGGTGCCCTTCCCATGGTAATGAGTGAGTTCTTGCTCTGTTAGTTCATGAGAGAGCTGATTGTTTAAAGGAGTCTGG;SVLEN=125;SVTYPE=CPX;TOTAL_MAPPINGS=1 56chr20 58695019 CPX_chr20:58695019-58695020 G <CPX> . . ALIGN_LENGTHS=82;ALT_ARRANGEMENT=UINS-72,chr20:58695237-58695339,UINS-83,chr20:58695287-58695340,UINS-12,chr20:58695229-58695328,UINS-27,chr20:58695237-58695320;CTG_NAMES=asm028638:tig00002;END=58695020;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=82;SEQ_ALT_HAPLOTYPE=TTGCGTGTGTATGAGTGCTGGTGTGTGCATGAATGGTGTGTGTGGTGTGTTTATGTGTGGTGTGTGTTGCTGTGTGAGTGCTGGTGTGTGCATGAGTGGCGTGTGTGTGGTGTGTGTTGCTGTGTGTGTATGAGTGTTGGTGTGTGCATGAGTGGTGTGTGTGTGCTGTGTGTATGTGTGGTGTGTGTTGCTGTGTATGAGTGTTGGTGTGTGCATGAGTGGTGTGTGTGTGCTGTGTGTACGTGTGTGTGTTGCTGTGTGTGTGTTTGAGTGCTGGTGTGTGCATGAGTGGTGTGTGTGTGGTGTGTGTGGTGTCTGTTGCTGTGTGTGTTTGAGTTCTGGTATGTGCATGAGTGGTGTGTGTGTGTGCTGTGTGTGTGGTGTGTTGCTGTGTGTGTATGAGTGCTGGTGTGTGCACGAGTGGTGTGTGTATTTGCGGTGTGTGTTGCTGTGTATATGTGAGTGCTGGTGTGTGCATGAGTGGCGTGTGTGGTGTGTATGTGTGGTGTGTGTTGCTGTTTGTGTTTGAGTGCTGATGTGTGCATGAGTGG;SVLEN=2;SVTYPE=CPX;TOTAL_MAPPINGS=1 57chr20 61375650 CPX_chr20:61375650-61376102 T <CPX> . . ALIGN_LENGTHS=1559;ALT_ARRANGEMENT=1,2,3,2,1,2,3;CTG_NAMES=asm028687:tig00001;END=61376102;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1559;SEGMENTS=chr20:61375650-61375759,chr20:61375759-61375874,chr20:61375874-61376102;SEQ_ALT_HAPLOTYPE=TGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTAGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGCTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGCTCTTGGTGCTGGTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGATGATGGTGGTGCTGGTGGTGGTCATAGCACTGGTGGTGATGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGATGATAGTGGGGTTTATTGATGGTAGTGTGATGGTCTTGGTGGTGCTGATAATGGTGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTGGCGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTATGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGGTGGTGATGATGTAGTTTGTTGATGGTAGCGTGATGTTCTTGGTGCTGGTGGTGGTGATGATGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGGTGGTGGTGGTGGTGATAGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGATGCTGGTGATGGTATTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTCGTGGTGGTGGTGTGGTTTGTCGATGGTAGTGTGGTGGTCTTGGTGCTGGTGGTTGTCGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGGTGGTGATGTGGTTTGTTGATGATAGTGTGATGGTCTTGGTGGTGGTAGTGATGGTGTGGTTTGCTGATGGTAGTGTGATGGTCTTGGTGGTGGTGATACTGTGGTTTGTGGATGGTAGTGTGATGGTCTTGGTGGTGATGGTGTGGTTTGTTGATGGTAGTGTGATGGTCTTGGTGCTGGTGG;SVLEN=453;SVTYPE=CPX;TOTAL_MAPPINGS=1 58chr20 61919906 CPX_chr20:61919906-61920109 T <CPX> . . ALIGN_LENGTHS=947;ALT_ARRANGEMENT=1,2,3,UINS-177,1,2,2,3;CTG_GOOD_NONCANONICAL_MAPPING=chr20_KI270869v1_alt,32261,-,1273M69I860M17D47M6D52M4D37M6D50M6D42M6D76M3I47M6D25M3I102M3D79M76H,60,193,2065;CTG_NAMES=asm028707:tig00000;END=61920109;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=947;SEGMENTS=chr20:61919906-61919908,chr20:61919908-61920054,chr20:61920054-61920109;SEQ_ALT_HAPLOTYPE=TCGTGATTATGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGCGGTGATTGCATGGAAGTGTGGTGTCACAGTGATTGCGTGGAAGCGTGTCGTGATTGTGTGGAAGCATGGTATCGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTGTGATTGTGTGGAAGCATGGTATCGTGATTGTGGAAGCGTGGTATCGCGGCGATTGTGTGGAAGCGTGGTGTCGCAGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGTGTGGAAGCATGGTGTCGTGATTGTGTGGAAGCATGTCGTGATTGTGTGGAAGTGTGATGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGGAAGTGTGGTGTCACGCTGATTGCATGGAAGTGTGTTGTGATTGTGTGGAAGCGTGATATCGCAGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATCGGAAGCGTGGTGTTGCGGTGATTGCATGGAAGCATGTTGTGATTGTGTGGAAGCATGGTATCGTGATTGTCTGGAAGCATGGTGTCATGGTGATTGGAAGTGTGTCGTGATTG;SVLEN=204;SVTYPE=CPX;TOTAL_MAPPINGS=1 59chr20 62452038 CPX_chr20:62452038-62452236 G <CPX> . . ALIGN_LENGTHS=235;ALT_ARRANGEMENT=1,UINS-148,1,2;CTG_NAMES=asm028732:tig00001;END=62452236;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=235;SEGMENTS=chr20:62452038-62452041,chr20:62452041-62452087,chr20:62452087-62452236;SEQ_ALT_HAPLOTYPE=GGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGAGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGAGAGGGAGGGTGAGAGTGGGGAGAGGGAGAGGGGAAGAAAGAGAG;SVLEN=199;SVTYPE=CPX;TOTAL_MAPPINGS=1 60chr20 63092255 CPX_chr20:63092255-63094246 G <CPX> . . ALIGN_LENGTHS=942;ALT_ARRANGEMENT=UINS-70,1;CTG_NAMES=asm028762:tig00002;END=63094246;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=942;SEGMENTS=chr20:63092256-63093346,chr20:63093346-63094246;SEQ_ALT_HAPLOTYPE=GGCCCAGGTTCCCGGGGCTGCGTGGGAGACACAGAAGTGGGGGCACCTCCGCAGCACCCACATCCTGCCGATGCCCAGGTTCCCGGGGCTGCGTGGGAGACACAGAAGTGGGGGCACCTCCGCAGCACCCACATCCTGCCGACGCCATGCACGTGAGTGTGCATGTGGGGCGGGGGTGCGCCAGGAAGGCAAAAATCCCAAATGTCAGCGCCCGGTGATTTGAGGAGTTCAGACAAAGCCTTCCCTGGGGCTGTCCTCGGCCCACTTCCCCATCATCCCAATGTCCCTGCAGCCCTTGAAATGGCTCGGATGTGGGGCAGGAGGGCTGGGCGGATGCTGATCTGAGGCCGAGGTTGATGGATTCCGGCTCCCCCAGTGCCGATCCGGCTGCTGCCCCACGTGGGGCTTTGAGGCTGCGGCAACAGAGCCGGTGGGACACGCTCCTGATGCCAGACCCAGGGGTAAGAGCTGCCCCTGCTCCACGGTCTGCGCCACGATGGCTGCCAGAGCGAAAATGGGAGGGAGAGAAGCGCTGTCAGGGCCTCCCAGGGAGGGTGTGTGGCGTGTGGCTTGCTAAGCACCCTCCTTTCTGATCCCGCCCTGAGCAGCTCCCTGGGACTTTTGTTGGTCAAAGCTTCAGCTGTGGTCAGAGGATCCAACGCTGCCGTCAACAGGCAGCTGCTGCCGTATGGCTGCAGACGTGGTTTCTGGAACAGACGGGCCCAGCCCTGCAAGGTGGGCTGGCTCTTTGGCTCTCGAGAGCACCACGGCACAGTGCTGATCTGGGTCCACACGGCCCAGCCACCCGGTCAGCTCGCCTGGTTCTTACATTTCCACTCCACAAACAGAACCCAGACCCAGATCTGCTTCCTCCGCCTCCCGCCCTCCTCGCCCCGCACCGTTTCTTGTCCCACAGAAGCTGTCATGGGTGCTGTGTACCCCATAGGGCGGGAGAGAAAGGTGTGTCCAGGAGCAATCTCGGGAAACAGGGGGCAGAGGATGCGGTGCAGAGCCGAGCTCCGGAGCCACCTTCCTGACCGCCAGAGCCTGACTGCATCCGTATGGCATGAGGTCGGTATCTAGGAGGCCATACTCTTTACCTAACATCCAGGACACAGGAAAAGGACGGAAACAGAAAAAAATACATAAATAAATTCAAGATGTC;SVLEN=1992;SVTYPE=CPX;TOTAL_MAPPINGS=1 61chr20 63353949 CPX_chr20:63353949-63354272 T <CPX> . . ALIGN_LENGTHS=81;ALT_ARRANGEMENT=2;CTG_NAMES=asm028777:tig00001;END=63354272;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=81;SEGMENTS=chr20:63353949-63354002,chr20:63354002-63354205,chr20:63354205-63354272;SEQ_ALT_HAPLOTYPE=TGGGGGGGAGCTGCTGTCCTAGGGGTGTTGTAGTCCTAGGGGGCTGTGGTCAGGCAAGAACTGTGATCCTTGTGGGGGCTGCAGTTCTGCAGGAGGCACTGTAGCCCTAGGGTGGGATGAAGTCCTGGGAGGACTGTGGTCCTGGCAGGGAATGTGGTCCTGGGGGCCTGTGGTCCTGGGGGGCTGTGGTCCTGGGGGAGCTGTGG;SVLEN=324;SVTYPE=CPX;TOTAL_MAPPINGS=1 62chr20 64096905 CPX_chr20:64096905-64097041 C <CPX> . . ALIGN_LENGTHS=166;ALT_ARRANGEMENT=1,1,UINS-166;CTG_NAMES=asm028821:tig00001;END=64097041;HQ_MAPPINGS=0;MAPPING_QUALITIES=54;MAX_ALIGN_LENGTH=166;SEGMENTS=chr20:64096905-64097041;SEQ_ALT_HAPLOTYPE=CCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACTGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGCCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAATCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACTATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACTACCATCATCATCACATTCATCATCACTATTACCATCATCATCACCACCATCACCATCACTATCACCACCATCATTACATTTGTCACCATCACCACCATTATCACCATCACCGCTATCACCACCACCACCGTC;SVLEN=137;SVTYPE=CPX;TOTAL_MAPPINGS=1 63chr21 21264944 CPX_chr21:21264944-21265096 T <CPX> . . ALIGN_LENGTHS=316,316;ALT_ARRANGEMENT=1,2,3,2,1,2,3;CTG_NAMES=asm029034:tig00000,asm029034:tig00001;END=21265096;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=316;SEGMENTS=chr21:21264944-21264988,chr21:21264988-21265052,chr21:21265052-21265096;SEQ_ALT_HAPLOTYPE=TATATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATATGTATATATACACATATATATTATATATATATGTGTCTGTATATATATACACATATATATTATATATATGTGTCTGTGTATATATATACACATATATATGTGTCTGTGTATATATGTACACATATATACTATATATGTGTATGTGTATATATATACACACATATATTATATAT;SVLEN=153;SVTYPE=CPX;TOTAL_MAPPINGS=2 64chr21 23428920 CPX_chr21:23428920-23429023 T <CPX> . . ALIGN_LENGTHS=1182,1182;ALT_ARRANGEMENT=UINS-84,2,3,UINS-5,2,2,3;CTG_NAMES=asm029052:tig00000,asm029052:tig00001;END=23429023;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=1182;SEGMENTS=chr21:23428920-23428968,chr21:23428968-23428998,chr21:23428998-23429023;SEQ_ALT_HAPLOTYPE=TATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATAATATATATAATATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATAT;SVLEN=104;SVTYPE=CPX;TOTAL_MAPPINGS=2 65chr21 26001843 CPX_chr21:26001843-26002386 A <CPX> . . ALIGN_LENGTHS=1370;ALT_ARRANGEMENT=-1;CTG_NAMES=asm029075:tig00000;END=26002386;HQ_MAPPINGS=1;MAPPING_QUALITIES=60;MAX_ALIGN_LENGTH=1370;SEGMENTS=chr21:26001844-26002384,chr21:26002384-26002386;SEQ_ALT_HAPLOTYPE=ACAATGTCAATACAAATGGGGACTAACTATTGTTTTACTTCCCTATACACGTTGCTCTTTCAGTAGATGCAATAAAGTACTGGTAAAACCAGAGGTGGCTACCATCACGATGATGTCAACAGGAGGGACAGTCAGCACTAAGCCCAGAAGGTGTCAAACACTCCGCAGGAGAAATGCGCCATGCAACGGACATGAAGATGATCTGACACTCTTCACGTGGTTTTCAGATGGAAACGTGGCTACGAAAGCATCAACCTCATTATCATCCATCATTAAGGCCATCTCACTCAGTACTGCTGCTTTCAAAGTCCACGCTCCCAAAGCAAATTGGATTTCTGTACACAATACTCTTACAGGATGAAACCCAACCAACTTGTTGACGTAAGTATCCCATCTACTTCGCAATTTTATTTATCTTCCAAAATTAAAGGACTGGCACCCTGATTTATTAAAAGTGAATTGGTTCTAGGGACCATATCCCCTCTGAGTTACTGACAGAGCAGCTTCTGGCCTGTGAAGCTCAAAGCCATGCCTAGATGTGAG;SVLEN=544;SVTYPE=CPX;TOTAL_MAPPINGS=1 66chr21 46069065 CPX_chr21:46069065-46069209 C <CPX> . . ALIGN_LENGTHS=154,154;ALT_ARRANGEMENT=UINS-59,1;CTG_NAMES=asm029362:tig00001,asm029362:tig00002;END=46069209;HQ_MAPPINGS=2;MAPPING_QUALITIES=60,60;MAX_ALIGN_LENGTH=154;SEGMENTS=chr21:46069066-46069156,chr21:46069156-46069209;SEQ_ALT_HAPLOTYPE=CCTAGGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGTGCATGTGTGCCTGGGTGTGTGTGCACGCCTGTGTGAGCATGTGTGCCTGGATGTGTGTGCATGTGTGTGCAA;SVLEN=145;SVTYPE=CPX;TOTAL_MAPPINGS=2 67