QUAST report
Loading...
Contigs are ordered from largest (contig #1) to smallest. Contigs are broken into nonoverlapping 100 bp windows. Plot shows numbers of windows for each GC percentage. |
{"date":"25 July 2014, Friday, 14:05:28","report":[["Statistics without reference",[{"values":[1,5,1,2,1,1,3],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[1,5,1,2,1,1,3],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[1,5,1,2,1,1,3],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[2162245,1340620,2151421,1189234,2149064,2150940,1659817],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[2162245,2140045,2151421,2146017,2149064,2150940,2148370],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[2162245,2140045,2151421,2146017,2149064,2150940,2148370],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[2162245,2140045,2151421,2146017,2149064,2150940,2148370],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[2162245,1340620,2151421,1189234,2149064,2150940,1659817],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[2162245,314959,2151421,956783,2149064,2150940,1659817],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,2,1,2,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["39.69","39.57","39.61","39.62","39.62","39.60","39.65"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[3,2,2,0,1,2,3],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[3,2,1,0,1,1,3],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0,1,0,0,1,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[1,1,1,0,1,1,1],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[2162245,1340620,2151421,0,2149064,2150940,1659817],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[4,5,4,4,4,4,36],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[123,46,44,44,45,44,37],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[33,23,20,21,20,21,41],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[87,73,64,66,64,109,458],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["5.70","2.15","2.05","2.05","2.10","2.05","1.74"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["1.53","1.08","0.93","0.98","0.93","0.98","1.93"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[29,21,19,20,19,19,27],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[4,2,1,1,1,2,14],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[1,3,2,3,3694,2,27242],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.05","0.14","0.09","0.14","171.89","0.09","1268.03"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.946","98.862","99.450","99.239","99.239","99.430","98.168"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.002","1.002","1.001","1.001","1.002","1.001","1.013"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["2297 + 4 part","2283 + 10 part","2297 + 4 part","2294 + 4 part","2294 + 4 part","2297 + 4 part","2257 + 22 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[1197408,869300,1189418,1188680,1188680,1189418,1234602],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[2162245,1340620,2151421,1189234,2149064,2150940,1659817],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[2162245,314959,2151421,956783,2149064,2150940,1659817],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[1197408,469127,1189418,1188680,1188680,1189418,1234602],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[959397,314959,959460,956783,956691,958979,483405],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[1197408,469127,1189418,1188680,1188680,1189418,1234602],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[959397,314959,959460,956783,956691,958979,483405],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,2,1,2,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[1,2,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[2,3,2,2,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[1,2,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[2,3,2,2,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[2160842,2160842,2160842,2160842,2160842,2160842,2160842],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["39.70","39.70","39.70","39.70","39.70","39.70","39.70"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[2301,2301,2301,2301,2301,2301,2301],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4,5,6],"assembliesNames":["alg_d3_web","alg_d3_raw","alg_d3_frac","alg_d3_50X","alg_d3_50X_Jumpall","alg_d3_100X","alg_d3_100X_Jumpall"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[2162245],[1340620,314959,280769,201288,2409],[2151421],[1189234,956783],[2149064],[2150940],[1659817,485690,2863]],"filenames":["alg_d3_web","alg_d3_raw","alg_d3_frac","alg_d3_50X","alg_d3_50X_Jumpall","alg_d3_100X","alg_d3_100X_Jumpall"]}
{"lists_of_lengths":[[1197408,959397,3248,2192],[869300,469127,314959,280769,201288,2409,2192],[1189418,959460,2543],[1188680,956783],[1188680,956691],[1189418,958979,2543],[1234602,483405,399053,2863,1010,454]],"filenames":["alg_d3_web","alg_d3_raw","alg_d3_frac","alg_d3_50X","alg_d3_50X_Jumpall","alg_d3_100X","alg_d3_100X_Jumpall"]}
{"assemblies_lengths":[2162245,2140045,2151421,2146017,2149064,2150940,2148370],"filenames":["alg_d3_web","alg_d3_raw","alg_d3_frac","alg_d3_50X","alg_d3_50X_Jumpall","alg_d3_100X","alg_d3_100X_Jumpall"]}
{"reflen":2160842}
{"ref_genes_number":2301,"genes_in_contigs":{"alg_d3_50X":[1255,1039],"alg_d3_100X":[2297],"alg_d3_raw":[1412,319,363,187,2],"alg_d3_50X_Jumpall":[2294],"alg_d3_100X_Jumpall":[1703,552,2],"alg_d3_web":[2297],"alg_d3_frac":[2297]},"filenames":["alg_d3_web","alg_d3_raw","alg_d3_frac","alg_d3_50X","alg_d3_50X_Jumpall","alg_d3_100X","alg_d3_100X_Jumpall"]}
{{ operonsInContigs }}
{"list_of_GC_distributions":[[[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],[0,0,0,0,0,0,0,0,0,0,0,0,1,3,2,2,2,9,6,16,40,46,69,89,133,171,226,261,349,394,451,515,635,716,686,836,989,977,1053,1200,1266,1313,1278,1249,1197,1083,940,854,703,531,389,296,193,143,109,67,38,36,24,10,16,3,2,4,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[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],[0,0,0,0,0,0,0,0,0,0,0,2,1,1,0,3,4,8,11,16,33,52,65,89,124,182,214,284,319,398,474,496,619,697,731,781,922,1072,1116,1202,1187,1318,1293,1247,1167,1096,988,835,684,513,367,263,180,119,97,47,38,18,15,4,1,4,3,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[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],[0,0,0,0,0,0,0,0,0,0,0,0,1,2,0,1,4,7,9,18,32,50,83,107,125,171,216,269,330,379,448,533,594,688,760,814,916,1025,1094,1240,1294,1211,1298,1237,1243,1179,955,781,639,503,392,301,207,121,95,65,24,17,11,10,3,5,3,3,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[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],[0,0,0,0,0,0,0,0,0,0,0,1,0,1,1,3,4,9,9,15,37,50,59,103,148,145,229,243,349,393,414,543,574,700,780,827,977,993,1102,1187,1244,1265,1237,1253,1234,1071,956,869,707,532,360,295,193,121,89,64,24,18,13,6,4,4,2,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[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],[0,0,0,0,0,0,0,0,0,0,0,0,2,1,0,4,2,9,11,14,32,46,80,102,133,185,192,259,319,387,459,530,602,609,764,858,933,995,1106,1216,1273,1320,1223,1282,1214,1080,978,817,676,519,388,295,182,144,84,52,32,13,13,7,0,5,4,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[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],[0,0,0,0,0,0,0,0,0,0,0,0,1,2,0,1,4,6,9,18,33,50,83,107,125,171,216,270,330,378,447,534,594,689,760,813,916,1024,1093,1242,1296,1208,1299,1235,1241,1181,956,781,641,504,392,301,205,121,95,60,25,17,11,10,3,4,3,3,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[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],[0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,4,3,12,9,26,27,47,60,110,121,144,190,264,334,389,470,523,593,649,769,775,857,1061,1091,1124,1242,1261,1290,1330,1218,1093,988,765,651,496,362,293,208,129,95,53,34,18,16,5,8,3,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null,"filenames":["alg_d3_web","alg_d3_raw","alg_d3_frac","alg_d3_50X","alg_d3_50X_Jumpall","alg_d3_100X","alg_d3_100X_Jumpall"]}
{
"# contigs" : "is the total number of contigs in the assembly.",
"Largest contig" : "is the length of the longest contig in the assembly.",
"Total length" : "is the total number of bases in the assembly.",
"Reference length" : "is the total number of bases in the reference.",
"N50" : "is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly. Usually there is no value that produces exactly 50%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 50% of the total assembly length.",
"NG50" : "is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the reference genome. This metric is computed only if a reference genome is provided.",
"N75" : "is the contig length such that using longer or equal length contigs produces 75% of the bases of the assembly. Usually there is no value that produces exactly 75%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 75% of the total assembly length.",
"NG75" : "is the contig length such that using longer or equal length contigs produces 75% of the bases of the reference genome. This metric is computed only if a reference genome is provided.",
"L50" : "is the minimum number of contigs that produce half (50%) of the bases of the assembly. In other words, it's the number of contigs of length at least N50.",
"LG50" : "is the minimum number of contigs that produce half (50%) of the bases of the reference genome. In other words, it's the number of contigs of length at least NG50. This metric is computed only if a reference genome is provided.",
"L75" : "is the minimum number of contigs that produce 75% of the bases of the assembly. In other words, it's the number of contigs of length at least N75.",
"LG75" : "is the minimum number of contigs that produce 75% of the bases of the reference genome. In other words, it's the number of contigs of length at least NG75. This metric is computed only if a reference genome is provided.",
"NA50" : "is N50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.",
"NGA50" : "is NG50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.",
"NA75" : "is N75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.",
"NGA75" : "is NG75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.",
"LA50" : "is L50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.",
"LGA50" : "is LG50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.",
"LA75" : "is L75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.",
"LGA75" : "is LG75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.",
"Average %IDY" : "is the average of alignment identity percent (Nucmer measure of alignment accuracy) among all contigs.",
"# misassemblies" : "is the number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (relocation) or they overlap on more than 1 kbp (relocation) or flanking sequences align on different strands (inversion) or different chromosomes (translocation).",
"# misassembled contigs" : "is the number of contigs that contain misassembly events.",
"Misassembled contigs length" : "is the number of total bases contained in all contigs that have one or more misassemblies.",
"# relocations" : "is the number of relocation events among all misassembly events. Relocation is a misassembly where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference, or they overlap by more than 1 kbp and both flanking sequences align on the same chromosome.",
"# translocations" : "is the number of translocation events among all misassembly events. Translocation is a misassembly where the flanking sequences align on different chromosomes.",
"# inversions" : "is the number of inversion events among all misassembly events. Inversion is a misassembly where it is not a relocation and the flanking sequences align on opposite strands of the same chromosome.",
"# local misassemblies" : "is the number of local misassemblies. We define a local misassembly breakpoint as a breakpoint that satisfies these conditions:
- Two or more distinct alignments cover the breakpoint.
- The gap between left and right flanking sequences is less than 1 kbp.
- The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.