Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:03:01 GMT 2023 |
| BAM file: | SRX7354235.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): | 44,093,041 / 44,050,564 |
| Number of aligned pairs (without duplicates): | 44,021,315 |
| Total number of alignments: | 95,133,010 |
| Number of secondary alignments: | 6,989,405 |
| Number of non-unique alignments: | 11,001,785 |
| Aligned to genes: | 73,772,847 |
| Ambiguous alignments: | 305,748 |
| No feature assigned: | 9,195,992 |
| Missing chromosome in annotation: | 856,638 |
| Not aligned: | 2,631,765 |
Reads genomic origin
| Exonic: | 73,772,847 / 88.92% |
| Intronic: | 6,043,231 / 7.28% |
| Intergenic: | 3,152,761 / 3.8% |
| Intronic/intergenic overlapping exon: | 3,703,126 / 4.46% |
Transcript coverage profile
| 5' bias: | 0.43 |
| 3' bias: | 0.29 |
| 5'-3' bias: | 1.64 |
Junction analysis
| Reads at junctions: | 25,856,141 |
| ACCT | 5.52% |
| AGGT | 4.55% |
| TCCT | 3.87% |
| ATCT | 3.8% |
| GCCT | 3.69% |
| AGGA | 3.05% |
| CCCT | 2.78% |
| AGCT | 2.64% |
| AGGC | 2.37% |
| TTCT | 2.29% |
| AGAT | 1.8% |
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