Using Small RNA Deep Sequencing Data to Detect Human Viruses
Table 2
HBV and HCV from the SRP002272 study.
Run ID
Sample_Source
Reference
Cov (%)
Depth
SRR039611
Human Normal Liver Tissue
NA
NA
NA
SRR039612
Human Normal Liver Tissue
NA
NA
NA
SRR039613
Human Normal Liver Tissue
NA
NA
NA
SRR039614
HBV-Infected Liver Tissue
JQ688405
423 (13.2)
3.0
SRR039615
Severe Chronic Hepatitis B Liver Tissue
NA
NA
NA
SRR039616
HBV(+) Distal Tissue
NA
NA
NA
SRR039617
HBV(+) Adjacent Tissue
NA
NA
NA
SRR039618
HBV(+) Side Tissue
NA
NA
NA
SRR039619
HBV(+) HCC Tissue
NA
NA
NA
SRR039620
HBV(+) Adjacent Tissue
JQ688404
1756 (54.6)
6.0
SRR039621
HBV(+) HCC Tissue
GQ475344
321 (10)
1.5
SRR039622
HCV(+) Adjacent Tissue
D85516
1032 (10.8)
1.8
SRR039623
HCV(+) HCC Tissue
GU133617
805 (8.3)
8.0
SRR039624
HBV(−) HCV(−) Adjacent Tissue
NA
NA
NA
SRR039625
HBV(−) HCV(−) HCC Tissue
NA
NA
NA
“Run ID” is uniq for each high-throughput fastq file in the NCBI SRA database. “Reference” uses the NCBI GenBank accession number. “Cov (%)” and “Depth” represent the genome coverage and the average depth, respectively. “Side Tissue” is close to the border between the tumor tissues and the normal tissues but 0–2 cm far from the tumor tissues. “Adjacent Tissue” is the normal tissues 2–5 cm far from the tumor tissues. “Distal Tissue” is the normal tissues at least 10cm far from the tumor tissues. “SRR039619” should have contained HBV but it was not found by our pipeline.
