Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:32:57 GMT 2023 |
| BAM file: | SRX7354182.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): | 35,894,703 / 35,836,714 |
| Number of aligned pairs (without duplicates): | 35,826,008 |
| Total number of alignments: | 76,153,681 |
| Number of secondary alignments: | 4,422,264 |
| Number of non-unique alignments: | 7,276,545 |
| Aligned to genes: | 58,668,088 |
| Ambiguous alignments: | 197,815 |
| No feature assigned: | 9,703,473 |
| Missing chromosome in annotation: | 307,760 |
| Not aligned: | 18,366,931 |
Reads genomic origin
| Exonic: | 58,668,088 / 85.81% |
| Intronic: | 6,506,344 / 9.52% |
| Intergenic: | 3,197,129 / 4.68% |
| Intronic/intergenic overlapping exon: | 2,551,209 / 3.73% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 2.13 |
Junction analysis
| Reads at junctions: | 20,735,196 |
| ACCT | 5.36% |
| AGGT | 4.9% |
| AGGA | 3.64% |
| ATCT | 3.57% |
| TCCT | 3.51% |
| GCCT | 2.77% |
| AGCT | 2.73% |
| AGGC | 2.47% |
| CCCT | 2.35% |
| AGAT | 2.28% |
| TTCT | 2.02% |
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