#
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