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test.txt_summary.html

test.txt_summary.html 36 KB
永久連結 文件歷史 原始文件

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  1. <html>
    2. 

  2. <head>
    3. 

  3.   <title>VEP summary</title>
    4. 

  4.   <script type="text/javascript" src="http://www.google.com/jsapi"></script>
    5. 

  5.   <script type="text/javascript">
    6. 

  6.     google.load('visualization', '1', {packages: ['corechart','table']});
    7. 

  7.   </script>
    8. 

  8.   <script type="text/javascript">
    9. 

  9.     
    10. 

  10.     function init() {
    11. 

  11.       // charts
    12. 

  12.       var var_class_pie = drawPie('var_class_pie', 'Variant classes', google.visualization.arrayToDataTable([['Variant class','Count'],['deletion',14],['insertion',15]]), null);
    13. 

  13. var var_class_table = drawTable('var_class_table', 'Variant classes', google.visualization.arrayToDataTable([['Variant class','Count'],['deletion',14],['insertion',15]]));
    14. 

  14. 

  15.           google.visualization.events.addListener(var_class_pie, 'select', function() {
    16. 

  16.             var_class_table.setSelection(var_class_pie.getSelection());
    17. 

  17.           });
    18. 

  18.           google.visualization.events.addListener(var_class_table, 'select', function() {
    19. 

  19.             var_class_pie.setSelection(var_class_table.getSelection());
    20. 

  20.           });
    21. 

  21.         var var_cons_pie = drawPie('var_cons_pie', 'Consequences (most severe)', google.visualization.arrayToDataTable([['Consequence type','Count'],['transcript_ablation',7],['stop_lost',1],['feature_elongation',1],['feature_truncation',1],['splice_polypyrimidine_tract_variant',2],['intron_variant',13],['upstream_gene_variant',2],['intergenic_variant',2]]), {slices: [{color: "#ff0000"}, {color: "#ff0000"}, {}, {}, {}, {color: "#02599c"}, {color: "#a2b5cd"}, {color: "gray"}]});
    22. 

  22. var var_cons_table = drawTable('var_cons_table', 'Consequences (most severe)', google.visualization.arrayToDataTable([['Consequence type','Count'],['transcript_ablation',7],['stop_lost',1],['feature_elongation',1],['feature_truncation',1],['splice_polypyrimidine_tract_variant',2],['intron_variant',13],['upstream_gene_variant',2],['intergenic_variant',2]]));
    23. 

  23. 

  24.           google.visualization.events.addListener(var_cons_pie, 'select', function() {
    25. 

  25.             var_cons_table.setSelection(var_cons_pie.getSelection());
    26. 

  26.           });
    27. 

  27.           google.visualization.events.addListener(var_cons_table, 'select', function() {
    28. 

  28.             var_cons_pie.setSelection(var_cons_table.getSelection());
    29. 

  29.           });
    30. 

  30.         var consequences_pie = drawPie('consequences_pie', 'Consequences (all)', google.visualization.arrayToDataTable([['Consequence type','Count'],['transcript_ablation',117],['stop_lost',10],['feature_elongation',1],['feature_truncation',46],['splice_polypyrimidine_tract_variant',19],['coding_sequence_variant',23],['5_prime_UTR_variant',11],['3_prime_UTR_variant',12],['non_coding_transcript_exon_variant',20],['intron_variant',183],['non_coding_transcript_variant',22],['upstream_gene_variant',21],['downstream_gene_variant',5],['intergenic_variant',2]]), {slices: [{color: "#ff0000"}, {color: "#ff0000"}, {}, {}, {}, {color: "#458b00"}, {}, {}, {}, {color: "#02599c"}, {}, {color: "#a2b5cd"}, {color: "#a2b5cd"}, {color: "gray"}]});
    31. 

  31. var consequences_table = drawTable('consequences_table', 'Consequences (all)', google.visualization.arrayToDataTable([['Consequence type','Count'],['transcript_ablation',117],['stop_lost',10],['feature_elongation',1],['feature_truncation',46],['splice_polypyrimidine_tract_variant',19],['coding_sequence_variant',23],['5_prime_UTR_variant',11],['3_prime_UTR_variant',12],['non_coding_transcript_exon_variant',20],['intron_variant',183],['non_coding_transcript_variant',22],['upstream_gene_variant',21],['downstream_gene_variant',5],['intergenic_variant',2]]));
    32. 

  32. 

  33.           google.visualization.events.addListener(consequences_pie, 'select', function() {
    34. 

  34.             consequences_table.setSelection(consequences_pie.getSelection());
    35. 

  35.           });
    36. 

  36.           google.visualization.events.addListener(consequences_table, 'select', function() {
    37. 

  37.             consequences_pie.setSelection(consequences_table.getSelection());
    38. 

  38.           });
    39. 

  39.         var coding_pie = drawPie('coding_pie', 'Coding consequences', google.visualization.arrayToDataTable([['Consequence type','Count'],['stop_lost',10],['coding_sequence_variant',23]]), {slices: [{color: "#ff0000"}, {color: "#458b00"}]});
    40. 

  40. var coding_table = drawTable('coding_table', 'Coding consequences', google.visualization.arrayToDataTable([['Consequence type','Count'],['stop_lost',10],['coding_sequence_variant',23]]));
    41. 

  41. 

  42.           google.visualization.events.addListener(coding_pie, 'select', function() {
    43. 

  43.             coding_table.setSelection(coding_pie.getSelection());
    44. 

  44.           });
    45. 

  45.           google.visualization.events.addListener(coding_table, 'select', function() {
    46. 

  46.             coding_pie.setSelection(coding_table.getSelection());
    47. 

  47.           });
    48. 

  48.         var chr_bar = drawBar('chr_bar', 'Variants by chromosome', google.visualization.arrayToDataTable([['Chromosome','Count'],['chr1',1],['chr4',1],['chr6',3],['chr7',4],['chr8',3],['chr9',1],['chr10',1],['chr12',2],['chr14',1],['chr16',3],['chr17',3],['chr18',1],['chr19',1],['chr22',2],['chrX',2]]), {legend: {position: "none"}});
    49. 

  49. var chr_table = drawTable('chr_table', 'Variants by chromosome', google.visualization.arrayToDataTable([['Chromosome','Count'],['chr1',1],['chr4',1],['chr6',3],['chr7',4],['chr8',3],['chr9',1],['chr10',1],['chr12',2],['chr14',1],['chr16',3],['chr17',3],['chr18',1],['chr19',1],['chr22',2],['chrX',2]]));
    50. 

  50. 

  51.           google.visualization.events.addListener(chr_bar, 'select', function() {
    52. 

  52.             chr_table.setSelection(chr_bar.getSelection());
    53. 

  53.           });
    54. 

  54.           google.visualization.events.addListener(chr_table, 'select', function() {
    55. 

  55.             chr_bar.setSelection(chr_table.getSelection());
    56. 

  56.           });
    57. 

  57.         var chr_chr1_area = drawArea('chr_chr1_area', 'Distribution of variants on chromosome chr1', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',0],['101',0],['102',0],['103',0],['104',0],['105',0],['106',0],['107',0],['108',0],['109',0],['110',0],['111',0],['112',0],['113',0],['114',0],['115',0],['116',0],['117',0],['118',0],['119',0],['120',0],['121',0],['122',0],['123',0],['124',0],['125',0],['126',0],['127',0],['128',0],['129',0],['130',0],['131',0],['132',0],['133',0],['134',0],['135',0],['136',0],['137',0],['138',0],['139',0],['140',0],['141',0],['142',0],['143',0],['144',0],['145',0],['146',0],['147',0],['148',0],['149',0],['150',0],['151',0],['152',0],['153',0],['154',0],['155',0],['156',0],['157',0],['158',0],['159',0],['160',0],['161',0],['162',0],['163',0],['164',0],['165',0],['166',0],['167',0],['168',0],['169',0],['170',0],['171',0],['172',0],['173',0],['174',0],['175',0],['176',0],['177',0],['178',0],['179',0],['180',0],['181',0],['182',0],['183',0],['184',0],['185',0],['186',0],['187',0],['188',0],['189',0],['190',0],['191',0],['192',0],['193',0],['194',0],['195',0],['196',0],['197',0],['198',0],['199',0],['200',0],['201',0],['202',0],['203',0],['204',0],['205',0],['206',0],['207',0],['208',0],['209',1],['210',0],['211',0],['212',0],['213',0],['214',0],['215',0],['216',0],['217',0],['218',0],['219',0],['220',0],['221',0],['222',0],['223',0],['224',0],['225',0],['226',0],['227',0],['228',0],['229',0],['230',0],['231',0],['232',0],['233',0],['234',0],['235',0],['236',0],['237',0],['238',0],['239',0],['240',0],['241',0],['242',0],['243',0],['244',0],['245',0],['246',0],['247',0],['248',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    58. 

  58. var chr_chr10_area = drawArea('chr_chr10_area', 'Distribution of variants on chromosome chr10', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',0],['101',0],['102',0],['103',0],['104',0],['105',1],['106',0],['107',0],['108',0],['109',0],['110',0],['111',0],['112',0],['113',0],['114',0],['115',0],['116',0],['117',0],['118',0],['119',0],['120',0],['121',0],['122',0],['123',0],['124',0],['125',0],['126',0],['127',0],['128',0],['129',0],['130',0],['131',0],['132',0],['133',0],['134',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    59. 

  59. var chr_chr12_area = drawArea('chr_chr12_area', 'Distribution of variants on chromosome chr12', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',2],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',0],['101',0],['102',0],['103',0],['104',0],['105',0],['106',0],['107',0],['108',0],['109',0],['110',0],['111',0],['112',0],['113',0],['114',0],['115',0],['116',0],['117',0],['118',0],['119',0],['120',0],['121',0],['122',0],['123',0],['124',0],['125',0],['126',0],['127',0],['128',0],['129',0],['130',0],['131',0],['132',0],['133',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    60. 

  60. var chr_chr14_area = drawArea('chr_chr14_area', 'Distribution of variants on chromosome chr14', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',1],['101',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    61. 

  61. var chr_chr16_area = drawArea('chr_chr16_area', 'Distribution of variants on chromosome chr16', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',2],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',1],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    62. 

  62. var chr_chr17_area = drawArea('chr_chr17_area', 'Distribution of variants on chromosome chr17', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',1],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',1],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',1],['84',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    63. 

  63. var chr_chr18_area = drawArea('chr_chr18_area', 'Distribution of variants on chromosome chr18', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',1],['80',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    64. 

  64. var chr_chr19_area = drawArea('chr_chr19_area', 'Distribution of variants on chromosome chr19', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',1],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    65. 

  65. var chr_chr22_area = drawArea('chr_chr22_area', 'Distribution of variants on chromosome chr22', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',1],['50',1],['51',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    66. 

  66. var chr_chr4_area = drawArea('chr_chr4_area', 'Distribution of variants on chromosome chr4', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',1],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',0],['101',0],['102',0],['103',0],['104',0],['105',0],['106',0],['107',0],['108',0],['109',0],['110',0],['111',0],['112',0],['113',0],['114',0],['115',0],['116',0],['117',0],['118',0],['119',0],['120',0],['121',0],['122',0],['123',0],['124',0],['125',0],['126',0],['127',0],['128',0],['129',0],['130',0],['131',0],['132',0],['133',0],['134',0],['135',0],['136',0],['137',0],['138',0],['139',0],['140',0],['141',0],['142',0],['143',0],['144',0],['145',0],['146',0],['147',0],['148',0],['149',0],['150',0],['151',0],['152',0],['153',0],['154',0],['155',0],['156',0],['157',0],['158',0],['159',0],['160',0],['161',0],['162',0],['163',0],['164',0],['165',0],['166',0],['167',0],['168',0],['169',0],['170',0],['171',0],['172',0],['173',0],['174',0],['175',0],['176',0],['177',0],['178',0],['179',0],['180',0],['181',0],['182',0],['183',0],['184',0],['185',0],['186',0],['187',0],['188',0],['189',0],['190',0],['191',0],['192',0],['193',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    67. 

  67. var chr_chr6_area = drawArea('chr_chr6_area', 'Distribution of variants on chromosome chr6', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',1],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',0],['101',0],['102',0],['103',0],['104',0],['105',0],['106',0],['107',0],['108',0],['109',0],['110',0],['111',0],['112',0],['113',0],['114',0],['115',0],['116',0],['117',0],['118',0],['119',0],['120',0],['121',0],['122',0],['123',0],['124',0],['125',0],['126',0],['127',0],['128',0],['129',0],['130',0],['131',0],['132',0],['133',0],['134',0],['135',0],['136',1],['137',0],['138',0],['139',0],['140',0],['141',0],['142',0],['143',0],['144',0],['145',0],['146',0],['147',0],['148',0],['149',0],['150',0],['151',0],['152',0],['153',0],['154',0],['155',0],['156',0],['157',0],['158',0],['159',0],['160',0],['161',0],['162',0],['163',0],['164',0],['165',0],['166',0],['167',0],['168',0],['169',0],['170',1],['171',0],['172',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    68. 

  68. var chr_chr7_area = drawArea('chr_chr7_area', 'Distribution of variants on chromosome chr7', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',1],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',1],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',0],['101',0],['102',0],['103',0],['104',0],['105',0],['106',0],['107',0],['108',0],['109',0],['110',0],['111',0],['112',0],['113',0],['114',0],['115',0],['116',0],['117',0],['118',0],['119',0],['120',0],['121',0],['122',0],['123',0],['124',0],['125',0],['126',0],['127',0],['128',0],['129',0],['130',0],['131',0],['132',0],['133',0],['134',0],['135',0],['136',0],['137',0],['138',0],['139',0],['140',0],['141',0],['142',0],['143',1],['144',1],['145',0],['146',0],['147',0],['148',0],['149',0],['150',0],['151',0],['152',0],['153',0],['154',0],['155',0],['156',0],['157',0],['158',0],['159',0],['160',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    69. 

  69. var chr_chr8_area = drawArea('chr_chr8_area', 'Distribution of variants on chromosome chr8', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',1],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',1],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',0],['101',0],['102',0],['103',0],['104',0],['105',0],['106',0],['107',0],['108',0],['109',0],['110',0],['111',0],['112',0],['113',0],['114',0],['115',0],['116',0],['117',0],['118',0],['119',0],['120',0],['121',0],['122',0],['123',0],['124',0],['125',0],['126',0],['127',0],['128',0],['129',0],['130',0],['131',0],['132',0],['133',0],['134',0],['135',0],['136',0],['137',0],['138',0],['139',0],['140',0],['141',0],['142',0],['143',1],['144',0],['145',0],['146',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    70. 

  70. var chr_chr9_area = drawArea('chr_chr9_area', 'Distribution of variants on chromosome chr9', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',1],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',0],['101',0],['102',0],['103',0],['104',0],['105',0],['106',0],['107',0],['108',0],['109',0],['110',0],['111',0],['112',0],['113',0],['114',0],['115',0],['116',0],['117',0],['118',0],['119',0],['120',0],['121',0],['122',0],['123',0],['124',0],['125',0],['126',0],['127',0],['128',0],['129',0],['130',0],['131',0],['132',0],['133',0],['134',0],['135',0],['136',0],['137',0],['138',0],['139',0],['140',0],['141',0],['142',0],['143',0],['144',0],['145',0],['146',0],['147',0],['148',0],['149',0],['150',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    71. 

  71. var chr_chrX_area = drawArea('chr_chrX_area', 'Distribution of variants on chromosome chrX', google.visualization.arrayToDataTable([['Position (mb)','Count'],['0',0],['1',0],['2',0],['3',0],['4',0],['5',0],['6',0],['7',0],['8',0],['9',0],['10',0],['11',0],['12',0],['13',0],['14',0],['15',0],['16',0],['17',0],['18',0],['19',0],['20',0],['21',0],['22',0],['23',0],['24',0],['25',0],['26',0],['27',0],['28',0],['29',0],['30',0],['31',0],['32',0],['33',0],['34',0],['35',0],['36',0],['37',0],['38',0],['39',0],['40',0],['41',0],['42',0],['43',0],['44',0],['45',0],['46',0],['47',0],['48',0],['49',0],['50',0],['51',0],['52',0],['53',0],['54',0],['55',0],['56',0],['57',0],['58',0],['59',0],['60',0],['61',0],['62',0],['63',0],['64',0],['65',0],['66',0],['67',0],['68',0],['69',0],['70',0],['71',0],['72',0],['73',0],['74',0],['75',0],['76',0],['77',0],['78',0],['79',0],['80',0],['81',0],['82',0],['83',0],['84',0],['85',0],['86',0],['87',0],['88',0],['89',0],['90',0],['91',0],['92',0],['93',0],['94',0],['95',0],['96',0],['97',0],['98',0],['99',0],['100',0],['101',0],['102',0],['103',0],['104',0],['105',0],['106',0],['107',0],['108',0],['109',0],['110',0],['111',0],['112',0],['113',0],['114',0],['115',0],['116',0],['117',0],['118',0],['119',0],['120',0],['121',0],['122',0],['123',0],['124',0],['125',1],['126',0],['127',0],['128',0],['129',0],['130',0],['131',0],['132',0],['133',0],['134',0],['135',0],['136',0],['137',0],['138',0],['139',0],['140',0],['141',0],['142',1],['143',0],['144',0],['145',0],['146',0],['147',0],['148',0],['149',0],['150',0],['151',0],['152',0],['153',0],['154',0]]), {hAxis: {title: "Position (mb)", textStyle: {fontSize: 8}}, legend: {position: "none"}});
    72. 

  72. var protein_bar = drawBar('protein_bar', 'Position in protein', google.visualization.arrayToDataTable([['Position in protein (percentile)','Count'],['00-10%',0],['10-20%',0],['20-30%',0],['30-40%',0],['40-50%',0],['50-60%',0],['60-70%',0],['70-80%',0],['80-90%',0],['90-100%',2]]), {hAxis: {title: "Position in protein (percentile)", textStyle: {fontSize: 10}}, legend: {position: "none"}});
    73. 

  73. 

  74.     }
    75. 

  75.     
    76. 

  76.     function drawPie(id, title, data, options) {    
    77. 

  77.       var pie = new google.visualization.PieChart(document.getElementById(id));
    78. 

  78.       pie.draw(data, options);
    79. 

  79.       return pie;
    80. 

  80.     }
    81. 

  81.     function drawBar(id, title, data, options) {
    82. 

  82.       var bar = new google.visualization.ColumnChart(document.getElementById(id));
    83. 

  83.       bar.draw(data, options);
    84. 

  84.       return bar;
    85. 

  85.     }
    86. 

  86.     function drawTable(id, title, data) {
    87. 

  87.       var table = new google.visualization.Table(document.getElementById(id));
    88. 

  88.       table.draw(data, null);
    89. 

  89.       return table;
    90. 

  90.     }
    91. 

  91.     function drawLine(id, title, data, options) {
    92. 

  92.       var line = new google.visualization.LineChart(document.getElementById(id));
    93. 

  93.       line.draw(data, options);
    94. 

  94.       return line;
    95. 

  95.     }
    96. 

  96.     function drawArea(id, title, data, options) {
    97. 

  97.       var area = new google.visualization.AreaChart(document.getElementById(id));
    98. 

  98.       area.draw(data, options);
    99. 

  99.       return area;
    100. 

  100.     }
    101. 

  101.     google.setOnLoadCallback(init);
    102. 

  102.   </script>
    103. 

  103.   
    104. 

  104.   
    105. 

  105.   <style type="text/css">
    106. 

  106.     body {
    107. 

  107.       font-family: arial, sans-serif;
    108. 

  108.       margin: 0px;
    109. 

  109.       padding: 0px;
    110. 

  110.     }
    111. 

  111.     
    112. 

  112.     a {color: #36b;}
    113. 

  113.     a.visited {color: #006;}
    114. 

  114.     
    115. 

  115.     .stats_table {
    116. 

  116.       margin: 5px;
    117. 

  117.       table-layout: fixed;
    118. 

  118.       width: 100%;
    119. 

  119.     }
    120. 

  120. 

  121.     pre {
    122. 

  122.       white-space: normal;
    123. 

  123.       word-break: keep-all;
    124. 

  124.     }
    125. 

  125. 

  126.     td {
    127. 

  127.       padding: 5px;
    128. 

  128.       word-break: break-word;
    129. 

  129.     }
    130. 

  130. 

  131.     td:nth-child(2) {
    132. 

  132.       width: 80%;
    133. 

  133.     }
    134. 

  134. 

  135.     th.gradient {
    136. 

  136.       height: auto;
    137. 

  137.     }
    138. 

  138. 

  139.     .stats_table tr:nth-child(odd) {
    140. 

  140.       background-color: #f0f0f0;
    141. 

  141.     }
    142. 

  142.     
    143. 

  143.     h3 {
    144. 

  144.       color: #666;
    145. 

  145.     }
    146. 

  146.     
    147. 

  147.     .masthead {
    148. 

  148.       background-color: white;
    149. 

  149.       color: rgb(204, 221, 255);
    150. 

  150.       height: 80px;
    151. 

  151.       width: 100%;
    152. 

  152.       padding: 0px;
    153. 

  153.     }
    154. 

  154.     
    155. 

  155.     .main {
    156. 

  156.       padding: 10px;
    157. 

  157.     }
    158. 

  158.     
    159. 

  159.     .gradient {
    160. 

  160.       background: #333366; /* Old browsers */
    161. 

  161.       background: -moz-linear-gradient(left,  #333366 0%, #ffffff 100%); /* FF3.6+ */
    162. 

  162.       background: -webkit-gradient(linear, left top, right top, color-stop(0%,#333366), color-stop(100%,#ffffff)); /* Chrome,Safari4+ */
    163. 

  163.       background: -webkit-linear-gradient(left,  #333366 0%,#ffffff 100%); /* Chrome10+,Safari5.1+ */
    164. 

  164.       background: -o-linear-gradient(left,  #333366 0%,#ffffff 100%); /* Opera 11.10+ */
    165. 

  165.       background: -ms-linear-gradient(left,  #333366 0%,#ffffff 100%); /* IE10+ */
    166. 

  166.       background: linear-gradient(to right,  #333366 0%,#ffffff 100%); /* W3C */
    167. 

  167.       filter: progid:DXImageTransform.Microsoft.gradient( startColorstr='#333366', endColorstr='#ffffff',GradientType=1 ); /* IE6-9 */
    168. 

  168.       
    169. 

  169.       padding: 0px;
    170. 

  170.       height: 80px;
    171. 

  171.       width: 700px;
    172. 

  172.     }
    173. 

  173.     
    174. 

  174.     .main_content {
    175. 

  175.       margin-left: 300px;
    176. 

  176.     }
    177. 

  177.     
    178. 

  178.     .sidemenu {
    179. 

  179.       width: 260px;
    180. 

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  212. <div class="sidemenu"><div class="sidemenu_head">Links</div><div class="sidemenu_body"><ul><li><a href="#masthead">Top of page</a></li><li><a href="#run_stats">VEP run statistics</a></li><li><a href="#data_version">Data version</a></li><li><a href="#gen_stats">General statistics</a></li><li><a href="#var_class">Variant classes</a></li><li><a href="#var_cons">Consequences (most severe)</a></li><li><a href="#consequences">Consequences (all)</a></li><li><a href="#coding">Coding consequences</a></li><li><a href="#chr">Variants by chromosome</a></li><li><a href="#protein">Position in protein</a></li></ul></div></div><div class='main_content'><h3 id="run_stats">VEP run statistics</h3><table class="stats_table"><tr><td>VEP version (API)</td><td> 112.0 (112)</td></tr><tr><td>Annotation sources</td><td>Cache: <kbd>/data/ref/hs1/vepcache/homo_sapiens/112</kbd>; Custom: /data/ref/hs1/chm13v2.0_RefSeq_Liftoff_v5.1_sorted.gff3.gz (overlap)</td></tr><tr><td>Species</td><td>homo_sapiens</td></tr><tr><td>Command line options</td><td><pre>--cache  --dir_cache /data/ref/hs1/vepcache/ --fasta /data/ref/hs1/chm13v2.0.fa --gff /data/ref/hs1/chm13v2.0_RefSeq_Liftoff_v5.1_sorted.gff3.gz --hgvs --input_file /data/longreads_basic_pipe/CAMARA/diag/nanomonsv/CAMARA_diag_nanomonsv_PASSED.vcf.gz --offline --output_file ./test.txt --plugin SpliceRegion --plugin Downstream --symbol</pre></td></tr><tr><td>Start time</td><td>2024-10-31 12:54:53</td></tr><tr><td>End time</td><td>2024-10-31 12:54:57</td></tr><tr><td>Run time</td><td>4 seconds</td></tr><tr><td>Input file</td><td><pre>/data/longreads_basic_pipe/CAMARA/diag/nanomonsv/CAMARA_diag_nanomonsv_PASSED.vcf.gz</pre></td></tr><tr><td>Output file</td><td><pre>./test.txt</pre></td></tr></table><h3 id="data_version">Data version</h3>No data version information available.<h3 id="gen_stats">General statistics</h3><table class="stats_table"><tr><td>Lines of input read</td><td>29</td></tr><tr><td>Variants processed</td><td>29</td></tr><tr><td>Variants filtered out</td><td>0</td></tr><tr><td>Novel / existing variants</td><td>-</td></tr><tr><td>Overlapped genes</td><td>113</td></tr><tr><td>Overlapped transcripts</td><td>295</td></tr><tr><td>Overlapped regulatory features</td><td>-</td></tr></table><hr/><h3 id="var_class">Variant classes</h3><div id="var_class_pie" style="width: 800px; height: 200px">&nbsp;</div><div id="var_class_table" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="var_cons">Consequences (most severe)</h3><div id="var_cons_pie" style="width: 800px; height: 400px">&nbsp;</div><div id="var_cons_table" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="consequences">Consequences (all)</h3><div id="consequences_pie" style="width: 800px; height: 400px">&nbsp;</div><div id="consequences_table" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="coding">Coding consequences</h3><div id="coding_pie" style="width: 800px; height: 400px">&nbsp;</div><div id="coding_table" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr">Variants by chromosome</h3><div id="chr_bar" style="width: 800px; height: 200px">&nbsp;</div><div id="chr_table" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr1">Distribution of variants on chromosome chr1</h3><div id="chr_chr1_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr10">Distribution of variants on chromosome chr10</h3><div id="chr_chr10_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr12">Distribution of variants on chromosome chr12</h3><div id="chr_chr12_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr14">Distribution of variants on chromosome chr14</h3><div id="chr_chr14_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr16">Distribution of variants on chromosome chr16</h3><div id="chr_chr16_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr17">Distribution of variants on chromosome chr17</h3><div id="chr_chr17_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr18">Distribution of variants on chromosome chr18</h3><div id="chr_chr18_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr19">Distribution of variants on chromosome chr19</h3><div id="chr_chr19_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr22">Distribution of variants on chromosome chr22</h3><div id="chr_chr22_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr4">Distribution of variants on chromosome chr4</h3><div id="chr_chr4_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr6">Distribution of variants on chromosome chr6</h3><div id="chr_chr6_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr7">Distribution of variants on chromosome chr7</h3><div id="chr_chr7_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr8">Distribution of variants on chromosome chr8</h3><div id="chr_chr8_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chr9">Distribution of variants on chromosome chr9</h3><div id="chr_chr9_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="chr_chrX">Distribution of variants on chromosome chrX</h3><div id="chr_chrX_area" style="width: 800px; height: 200px">&nbsp;</div><hr/><h3 id="protein">Position in protein</h3><div id="protein_bar" style="width: 800px; height: 200px">&nbsp;</div></div>
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