Input data and parameters
Input
Analysis date: | Tue Oct 31 01:30:23 GMT 2023 |
BAM file: | SRX7354279.markdup.sorted.bam |
Counting algorithm: | uniquely-mapped-reads |
GTF file: | gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf |
Number of bases for 5'-3' bias computation: | 100 |
Number of transcripts for 5'-3' bias computation: | 1,000 |
Paired-end sequencing: | yes |
Protocol: | strand-specific-reverse |
Sorting performed: | yes |
Summary
Reads alignment
Number of mapped reads (left/right): | 46,172,871 / 46,099,030 |
Number of aligned pairs (without duplicates): | 46,093,401 |
Total number of alignments: | 100,905,897 |
Number of secondary alignments: | 8,633,996 |
Number of non-unique alignments: | 11,029,229 |
Aligned to genes: | 72,445,730 |
Ambiguous alignments: | 382,782 |
No feature assigned: | 15,083,611 |
Missing chromosome in annotation: | 1,964,545 |
Not aligned: | 4,694,751 |
Reads genomic origin
Exonic: | 72,445,730 / 82.77% |
Intronic: | 12,974,879 / 14.82% |
Intergenic: | 2,108,732 / 2.41% |
Intronic/intergenic overlapping exon: | 3,196,992 / 3.65% |
Transcript coverage profile
5' bias: | 0.4 |
3' bias: | 0.23 |
5'-3' bias: | 1.64 |
Junction analysis
Reads at junctions: | 33,014,458 |
ACCT | 5% |
AGGT | 4.65% |
ATCT | 3.77% |
AGGA | 3.66% |
TCCT | 3.5% |
GCCT | 3.11% |
AGCT | 2.74% |
CCCT | 2.73% |
AGGC | 2.37% |
TTCT | 2.26% |
AGAT | 2.22% |