Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:40:57 GMT 2023 |
| BAM file: | SRX7354133.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): | 42,445,626 / 42,407,722 |
| Number of aligned pairs (without duplicates): | 42,378,182 |
| Total number of alignments: | 90,662,577 |
| Number of secondary alignments: | 5,809,229 |
| Number of non-unique alignments: | 9,632,655 |
| Aligned to genes: | 72,557,657 |
| Ambiguous alignments: | 305,713 |
| No feature assigned: | 7,676,029 |
| Missing chromosome in annotation: | 490,523 |
| Not aligned: | 3,006,678 |
Reads genomic origin
| Exonic: | 72,557,657 / 90.43% |
| Intronic: | 4,109,963 / 5.12% |
| Intergenic: | 3,566,066 / 4.44% |
| Intronic/intergenic overlapping exon: | 3,199,382 / 3.99% |
Transcript coverage profile
| 5' bias: | 0.35 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 22,718,935 |
| ACCT | 4.95% |
| AGGT | 4.71% |
| ATCT | 4.3% |
| TCCT | 3.95% |
| GCCT | 3.43% |
| AGGA | 3.2% |
| CCCT | 2.77% |
| AGCT | 2.49% |
| TTCT | 2.4% |
| AGGC | 2.3% |
| AGAA | 1.85% |
.png)
.png)
.png)
