Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:46:18 GMT 2023 |
| BAM file: | SRX7354337.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): | 45,382,998 / 45,357,785 |
| Number of aligned pairs (without duplicates): | 45,349,717 |
| Total number of alignments: | 98,239,566 |
| Number of secondary alignments: | 7,498,783 |
| Number of non-unique alignments: | 11,755,771 |
| Aligned to genes: | 77,851,350 |
| Ambiguous alignments: | 337,985 |
| No feature assigned: | 7,428,333 |
| Missing chromosome in annotation: | 866,127 |
| Not aligned: | 3,206,967 |
Reads genomic origin
| Exonic: | 77,851,350 / 91.29% |
| Intronic: | 4,084,640 / 4.79% |
| Intergenic: | 3,343,693 / 3.92% |
| Intronic/intergenic overlapping exon: | 4,046,270 / 4.74% |
Transcript coverage profile
| 5' bias: | 0.09 |
| 3' bias: | 0.11 |
| 5'-3' bias: | 2.35 |
Junction analysis
| Reads at junctions: | 27,388,871 |
| TCCT | 6.45% |
| ACCT | 5.67% |
| ATCT | 4.76% |
| AGGT | 3.82% |
| CCCT | 3.77% |
| AGGA | 2.62% |
| TCCC | 2.47% |
| GCCT | 2.34% |
| CGTA | 2.22% |
| AGGC | 2.22% |
| GTCT | 2.11% |
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