Candidate Integration Site

The following tables show Integration site candidates with gene annotation(table description).


GeneName DistToGene HumanChr HIntegrationPos HChr HStart HPosition VirusID VStart VirusEnd DiscordantReads HumanSoftClipping HumanProperMappedReads ViralProperMappedReads ViralSoftClipping Coverage Score RepeatRegion
CCAT1 0 chr8 128230630 chr8 128230680 128230888 Humanpapillomavirus-18_9626069 5771 5972 1200 155 1322 824 157 6080 1273.69 N
CCAT1 1855 chr8 128233368 chr8 128233053 128233217 Humanpapillomavirus-18_9626069 2850 2959 124 15 2257 52 0 6654 121.245 N
CCAT1 2743 chr8 128234256 chr8 128233890 128234221 Humanpapillomavirus-18_9626069 7576 7825 130 229 1338 1103 153 5934 180.326 N
CCAT1 10036 chr8 128241549 chr8 128241184 128241499 Humanpapillomavirus-18_9626069 2190 2433 292 45 714 414 17 2766 235.732 N



Primer Design

The following tables show Primer design for the Integration Sites found(table description).


Event FWD_Sequence REV_Sequence FWD_TM REV_TM Product_Length Event FWD_Sequence REV_Sequence FWD_TM REV_TM Product_Length
LeftEvent_1 CACATAGCCATTGAAAACAA ATGGGAACTTTCAGTGTCAT 58.200 57.995 438 RightEvent_1 TCCTAAGGTTTCTGCATACC AAAACATGGAGACTGAGGAG 57.843 57.864 269
LeftEvent_2 CCATGTTTGGTGATGAGTTA GAATATTGCATTTTCCCAAC 57.963 57.958 206 RightEvent_2 ATTAGATTTGCACGAGGAAG TTGTTTCTTCATGTTTCCCT 57.995 58.200 255
LeftEvent_3 GTGAGACTCCCTCTCAAAAA GGGTAGACAGAATGTTGGAC 57.996 57.995 220 RightEvent_3 GTCCAACATTCTGTCTACCC GTGTTTGATGATAAATGGCA 57.995 57.983 161
LeftEvent_4 CCTCTGTCAACTCCCTGTAT TGCTGGTCCACAAAATACTA 57.731 57.785 187 RightEvent_4 AAAAATAGATGAAGGGGGAG TGCTCAAGACAGAAAATGAA 58.134 58.126 347


Circos plot showing Human Integration Sites

Circos plot showing Viral Sites with overlayed coverage data


Appendix


table description for Integration Site


1. GeneName - HUGO gene name
2. DistToGene - The reported distance for the nearest gene
3. HumanChr - Integration Site Human chromosome
4. HIntegrationPos - exact Genomic location of Human chromosome for integration site
5. HChr - Human chromosome for the region
6. HStart - Genomic Start position of the cluster
7. HPosition - Genomic End position of the cluster
8. VirusID - Virus Name
9. VStart - Genomic Start position of the viral cluster
10. VirusEnd - Genomic End position of the viral cluster
11. DiscordantReads - # of same read pair mapping to human cluster and Viral Cluster
12. SoftclippingReads - # of reads having Soft clip bases more than threshold
13. RepeatRegion - If the region falls in repeat region


table description for Primer design


1. Event - event ID
2. FWD_Sequence - left primer (before integration site within human genome for pair 1)/ (before integration site within viral genome for pair 2)
3. REV_Sequence - right primer (after integration site within viral genome for pair 1)/ (after integration site within human genome for pair 2)
4. FWD_TM - the predicated melting temperature of the left primer
5. REV_TM - the predicated melting temperature of the right primer
6. Product_Length - the length of the region being amplified