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1. Location and orientation of sequence contigs against map

1. Location and orientation of sequence contigs against map. 2. contig 112, 117, 118 (a) alignments. middle region of 118 matches map but left end matches a different region of map (slide 6) and right end doesn’t match anywhere – mis-assembly?. Gap = ~7 kb. Gap = ~2 kb?.

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1. Location and orientation of sequence contigs against map

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  1. 1. Location and orientation of sequence contigs against map

  2. 2. contig 112, 117, 118 (a) alignments middle region of 118 matches map but left end matches a different region of map (slide 6) and right end doesn’t match anywhere – mis-assembly? Gap = ~7 kb Gap = ~2 kb? Approx 62 kb gap to 94 Good matches for contigs 112 and 117 (in reverse orientation relative to slide 1)

  3. Poor match between 115 and map in reverse orientation – either false “match” or possible mis-assembly Poor match between 115 and map – either false “match” or possible mis-assembly 3. contig 94, 98, 101, 107, 115 alignments Strong matches between 96, 107, and map – moderate match with 101 - see next slide

  4. 4. contig 96, 101, 107 alignments Approx 60 kb gap between 107 and 105 Gap ~ 21kb If this 1.2 kb fragment in 101 is “missing” from map, then 101 would show strong match with map and the left-most fragment of 101 would then lie very close to the right end of Contig 96 (within <2 kb) “missing” small fragments from map would further strengthen alignment of 107

  5. 5. contig 105, 110, 114 alignments If this 1.2 kb fragment in 105 is “missing” from the map, then 105 would show strong match with map and the right end of 105 would lie very close (~1.2 kb) to the left end of 110 Left end of 114 shows strong match with a different region of the map – mis-assembly? (See slide 7) Very small fragments “missing” from the map would bring left end of contig 110 into strong alignment and place it very close to right end of 105, but right end of 110 matches no part of map - mis-assembly? Middle region of 114 shows strong match with map except that map predicts single fragment of 3491 bp here whereas 114 shows two fragments totaling 3425 bp - possible base mis-call to create false site in 114?

  6. 6. contig 97, 99 and 118 (b) alignments 99 shows strong match 97 shows moderate match (Reverse orientation) Gap ~ 18 kb 27 kb gap between 99 and 102 Left end of 118 shows very strong match with map but middle region matches different region of map (see slide 2) Mis-assembly?

  7. 7. contig 102, 103, 106, 114 alignments 103 shows a large fragment, not present in the map. Sequence assembly error? or possibly base mis-call appearing as “missing site” in 103? 103 shows small fragment not present in the map. “missing fragment” map error? Strong match for 106 (reverse orientation) Gap ~ 15 kb Gap ~ 25 kb Gap ~ 41 kb Strong match for right end of 114, but left end matches different part of map – (see slide 5) - mis-assembly?

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