Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:57:01 GMT 2023 |
| BAM file: | SRX7354407.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): | 52,372,451 / 52,318,207 |
| Number of aligned pairs (without duplicates): | 52,310,149 |
| Total number of alignments: | 111,082,708 |
| Number of secondary alignments: | 6,392,050 |
| Number of non-unique alignments: | 10,618,652 |
| Aligned to genes: | 87,946,642 |
| Ambiguous alignments: | 342,128 |
| No feature assigned: | 11,752,448 |
| Missing chromosome in annotation: | 422,838 |
| Not aligned: | 8,777,822 |
Reads genomic origin
| Exonic: | 87,946,642 / 88.21% |
| Intronic: | 8,038,926 / 8.06% |
| Intergenic: | 3,713,522 / 3.72% |
| Intronic/intergenic overlapping exon: | 3,548,548 / 3.56% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.88 |
Junction analysis
| Reads at junctions: | 31,453,401 |
| ACCT | 5.34% |
| AGGT | 4.74% |
| AGGA | 3.58% |
| ATCT | 3.52% |
| TCCT | 3.39% |
| GCCT | 3.05% |
| AGCT | 2.78% |
| AGGC | 2.39% |
| CCCT | 2.3% |
| AGAT | 2.26% |
| TTCT | 2.19% |
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