Mercurial > repos > thondeboer > neat_genreads

annotate test-data/chrMT-PE-VCF-BAM-panic.vcf @ 7:fc1c7b6fb7b6 draft

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planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
author thondeboer
date Tue, 15 May 2018 18:12:29 -0400
parents 6e75a84e9338
children
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1 ##fileformat=VCFv4.1
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2 ##reference=chrMT.fa
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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4 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
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5 ##INFO=<ID=VMX,Number=1,Type=String,Description="SNP is Missense in these Read Frames">
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6 ##INFO=<ID=VNX,Number=1,Type=String,Description="SNP is Nonsense in these Read Frames">
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7 ##INFO=<ID=VFX,Number=1,Type=String,Description="Indel Causes Frameshift">
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8 ##INFO=<ID=WP,Number=A,Type=Integer,Description="NEAT-GenReads ploidy indicator">
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9 ##ALT=<ID=DEL,Description="Deletion">
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10 ##ALT=<ID=DUP,Description="Duplication">
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11 ##ALT=<ID=INS,Description="Insertion of novel sequence">
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12 ##ALT=<ID=INV,Description="Inversion">
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13 ##ALT=<ID=CNV,Description="Copy number variable region">
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14 ##ALT=<ID=TRANS,Description="Translocation">
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15 ##ALT=<ID=INV-TRANS,Description="Inverted translocation">
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16 #CHROM POS ID REF ALT QUAL FILTER INFO
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427 MT 11933 . A G . PASS WP=0/1/0
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428 MT 11968 . A G . PASS WP=1/0/0
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429 MT 12054 . G A . PASS WP=1/0/0
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430 MT 12104 . C G . PASS WP=0/0/1
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431 MT 12136 . T C . PASS WP=0/0/1
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432 MT 12207 . G A . PASS WP=1/0/0
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433 MT 12243 . TGT T . PASS WP=0/0/1
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434 MT 12256 . G A . PASS WP=0/1/0
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435 MT 12309 . A G . PASS WP=0/0/1
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436 MT 12341 . C G . PASS WP=1/0/0
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437 MT 12399 . C T . PASS WP=0/1/0
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438 MT 12402 . C T . PASS WP=0/0/1
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439 MT 12433 . C T . PASS WP=1/0/0
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440 MT 12472 . A G . PASS WP=0/1/0
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441 MT 12481 . T TAAC . PASS WP=0/1/0
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442 MT 12500 . T G . PASS WP=0/1/0
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443 MT 12576 . C T . PASS WP=0/1/0
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444 MT 12577 . A G . PASS WP=1/0/0
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445 MT 12783 . TATA T . PASS WP=0/0/1
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446 MT 12789 . C T . PASS WP=0/0/1
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447 MT 12790 . T C . PASS WP=0/0/1
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448 MT 12793 . T A . PASS WP=0/0/1
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449 MT 12814 . G A . PASS WP=1/0/0
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450 MT 12907 . C T . PASS WP=0/0/1
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451 MT 12910 . C T . PASS WP=0/1/0
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452 MT 12929 . C A . PASS WP=0/0/1
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453 MT 13002 . C T . PASS WP=0/1/0
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454 MT 13003 . A G . PASS WP=1/0/0
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455 MT 13016 . T C . PASS WP=1/0/0
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456 MT 13017 . A G . PASS WP=1/0/0
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457 MT 13024 . C T . PASS WP=0/1/0
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458 MT 13094 . T A . PASS WP=1/0/0
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459 MT 13103 . G GA . PASS WP=0/1/0
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460 MT 13232 . A G . PASS WP=0/0/1
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461 MT 13263 . A G . PASS WP=0/0/1
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462 MT 13265 . T G . PASS WP=0/1/0
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463 MT 13289 . G A . PASS WP=0/0/1
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464 MT 13298 . A G . PASS WP=0/0/1
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465 MT 13310 . CATT C . PASS WP=0/0/1
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466 MT 13323 . C T . PASS WP=0/1/0
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467 MT 13344 . AGCCA A . PASS WP=1/0/0
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468 MT 13369 . T C . PASS WP=1/0/0
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469 MT 13380 . C CGTC . PASS WP=0/1/0
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470 MT 13384 . C A . PASS WP=0/0/1
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471 MT 13386 . T C . PASS WP=1/0/0
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472 MT 13411 . A G . PASS WP=0/1/0
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473 MT 13462 . G A . PASS WP=0/1/0
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474 MT 13488 . T A . PASS WP=1/0/0
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475 MT 13493 . T G . PASS WP=0/1/0
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476 MT 13501 . T TCGTCT . PASS WP=0/0/1
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477 MT 13617 . T C . PASS WP=0/0/1
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478 MT 13619 . T C . PASS WP=0/1/0
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479 MT 13639 . CCT C . PASS WP=0/0/1
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480 MT 13672 . AA A . PASS WP=0/0/1
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481 MT 13758 . C T . PASS WP=0/0/1
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482 MT 13763 . C A . PASS WP=0/0/1
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483 MT 13787 . T G . PASS WP=0/0/1
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484 MT 13808 . T A . PASS WP=0/0/1
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485 MT 13894 . T C . PASS WP=0/1/0
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486 MT 13941 . C T . PASS WP=0/1/0
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487 MT 13943 . C A . PASS WP=0/1/0
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488 MT 14005 . T C . PASS WP=0/1/0
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489 MT 14008 . C T . PASS WP=1/0/0
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490 MT 14060 . T G . PASS WP=1/0/0
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491 MT 14067 . C T . PASS WP=1/0/0
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492 MT 14114 . T TA . PASS WP=1/0/0
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493 MT 14137 . C T . PASS WP=1/0/0
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494 MT 14175 . C T . PASS WP=0/1/0
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495 MT 14187 . C A . PASS WP=0/1/0
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496 MT 14242 . A G . PASS WP=0/0/1
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497 MT 14326 . T C . PASS WP=1/1/1
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498 MT 14356 . C T . PASS WP=0/1/0
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parents:
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499 MT 14373 . C T . PASS WP=0/1/0
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thondeboer
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500 MT 14383 . C CTTCGTCC . PASS WP=1/0/0
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501 MT 14405 . A G . PASS WP=0/0/1
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thondeboer
parents:
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502 MT 14410 . G A . PASS WP=0/1/0
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thondeboer
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503 MT 14460 . C T . PASS WP=0/1/0
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504 MT 14492 . C G . PASS WP=1/0/0
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505 MT 14520 . C A . PASS WP=1/0/0
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parents:
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506 MT 14522 . A G . PASS WP=0/1/0
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507 MT 14595 . A G . PASS WP=0/1/0
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508 MT 14612 . G A . PASS WP=1/0/0
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parents:
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509 MT 14653 . C T . PASS WP=0/0/1
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510 MT 14665 . A G . PASS WP=1/0/0
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511 MT 14673 . T C . PASS WP=1/0/0
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512 MT 14699 . A G . PASS WP=0/1/0
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513 MT 14703 . A T . PASS WP=1/0/0
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514 MT 14727 . T C . PASS WP=0/1/0
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515 MT 14740 . A G . PASS WP=0/0/1
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516 MT 14807 . CT C . PASS WP=1/0/0
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517 MT 14809 . C T . PASS WP=1/0/0
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518 MT 14831 . G A . PASS WP=0/0/1
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519 MT 14851 . A G . PASS WP=1/0/0
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520 MT 14895 . T C . PASS WP=1/0/0
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521 MT 14900 . G A . PASS WP=0/1/0
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522 MT 14941 . A G . PASS WP=0/1/0
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523 MT 15009 . C T . PASS WP=0/1/0
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524 MT 15050 . C CAAGGCATAT . PASS WP=0/1/0
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525 MT 15066 . T C . PASS WP=1/0/0
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526 MT 15073 . C T . PASS WP=0/0/1
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527 MT 15081 . C T . PASS WP=0/0/1
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528 MT 15110 . GCAACT G . PASS WP=0/0/1
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529 MT 15123 . C G . PASS WP=0/0/1
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parents:
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530 MT 15123 . C T . PASS WP=0/1/0
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531 MT 15125 . G A . PASS WP=1/0/0
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532 MT 15190 . C T . PASS WP=1/0/0
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533 MT 15231 . A G . PASS WP=0/1/0
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534 MT 15234 . G A . PASS WP=0/0/1
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thondeboer
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535 MT 15270 . T A . PASS WP=0/0/1
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536 MT 15280 . C T . PASS WP=0/0/1
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thondeboer
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537 MT 15293 . T C . PASS WP=0/1/0
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thondeboer
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538 MT 15307 . C T . PASS WP=0/1/0
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thondeboer
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539 MT 15311 . A AT . PASS WP=0/1/0
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thondeboer
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540 MT 15317 . G A . PASS WP=0/1/0
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thondeboer
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541 MT 15324 . C T . PASS WP=1/0/0
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thondeboer
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542 MT 15375 . G A . PASS WP=1/0/0
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543 MT 15427 . A G . PASS WP=1/0/0
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thondeboer
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544 MT 15477 . T C . PASS WP=1/0/0
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thondeboer
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545 MT 15527 . C G . PASS WP=1/0/0
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thondeboer
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546 MT 15565 . T C . PASS WP=1/0/0
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thondeboer
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547 MT 15569 . C T . PASS WP=0/1/0
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thondeboer
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548 MT 15596 . G GAGTCC . PASS WP=1/0/0
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thondeboer
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549 MT 15608 . C G . PASS WP=1/0/0
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thondeboer
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550 MT 15611 . G C . PASS WP=0/1/0
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thondeboer
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551 MT 15683 . CA C . PASS WP=0/1/0
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thondeboer
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552 MT 15748 . T C . PASS WP=0/0/1
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thondeboer
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553 MT 15762 . G A . PASS WP=1/0/0
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thondeboer
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554 MT 15807 . C T . PASS WP=1/0/0
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thondeboer
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555 MT 15822 . T G . PASS WP=0/0/1
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thondeboer
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556 MT 15833 . C A . PASS WP=0/0/1
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thondeboer
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557 MT 15847 . A G . PASS WP=0/1/0
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thondeboer
parents:
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558 MT 15957 . C T . PASS WP=1/0/0
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thondeboer
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559 MT 15968 . T C . PASS WP=1/0/0
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thondeboer
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560 MT 15997 . T C . PASS WP=0/0/1
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thondeboer
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561 MT 15999 . A C . PASS WP=0/0/1
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thondeboer
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562 MT 16062 . A G . PASS WP=0/1/0
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thondeboer
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563 MT 16067 . C T . PASS WP=0/0/1
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thondeboer
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564 MT 16088 . T C . PASS WP=0/0/1
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thondeboer
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565 MT 16116 . A G . PASS WP=1/0/0
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thondeboer
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566 MT 16132 . A G . PASS WP=0/1/0
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thondeboer
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567 MT 16201 . C A . PASS WP=1/0/0
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thondeboer
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568 MT 16203 . A T . PASS WP=0/1/0
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thondeboer
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569 MT 16217 . T C . PASS WP=1/0/0
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thondeboer
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570 MT 16228 . C T . PASS WP=1/0/0
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thondeboer
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571 MT 16266 . C T . PASS WP=0/1/0
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thondeboer
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572 MT 16274 . G A . PASS WP=0/0/1
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thondeboer
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573 MT 16277 . A C . PASS WP=0/0/1
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thondeboer
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574 MT 16295 . C T . PASS WP=0/0/1
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thondeboer
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575 MT 16301 . C T . PASS WP=0/1/0
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thondeboer
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576 MT 16308 . T C . PASS WP=1/1/1
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thondeboer
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577 MT 16345 . A T . PASS WP=1/0/0
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thondeboer
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578 MT 16390 . G A . PASS WP=1/0/0
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thondeboer
parents:
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579 MT 16409 . T C . PASS WP=0/1/0
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thondeboer
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580 MT 16413 . T C . PASS WP=0/1/0
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thondeboer
parents:
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581 MT 16555 . T C . PASS WP=0/0/1