Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:12:57 GMT 2023 |
| BAM file: | SRX7354269.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): | 34,884,078 / 34,870,025 |
| Number of aligned pairs (without duplicates): | 34,866,999 |
| Total number of alignments: | 74,741,199 |
| Number of secondary alignments: | 4,987,096 |
| Number of non-unique alignments: | 7,684,640 |
| Aligned to genes: | 57,287,424 |
| Ambiguous alignments: | 199,215 |
| No feature assigned: | 8,863,934 |
| Missing chromosome in annotation: | 705,986 |
| Not aligned: | 1,688,861 |
Reads genomic origin
| Exonic: | 57,287,424 / 86.6% |
| Intronic: | 4,992,328 / 7.55% |
| Intergenic: | 3,871,606 / 5.85% |
| Intronic/intergenic overlapping exon: | 2,251,901 / 3.4% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.27 |
| 5'-3' bias: | 1.82 |
Junction analysis
| Reads at junctions: | 18,958,295 |
| AGGT | 4.99% |
| ACCT | 4.98% |
| AGGA | 3.6% |
| TCCT | 3.4% |
| ATCT | 3.32% |
| GCCT | 2.88% |
| AGCT | 2.85% |
| AGGC | 2.51% |
| CCCT | 2.45% |
| AGAT | 2.17% |
| TTCT | 2.05% |
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