Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:50:04 GMT 2023 |
| BAM file: | SRX7354063.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): | 39,530,128 / 39,501,661 |
| Number of aligned pairs (without duplicates): | 39,493,746 |
| Total number of alignments: | 86,917,844 |
| Number of secondary alignments: | 7,886,055 |
| Number of non-unique alignments: | 11,367,644 |
| Aligned to genes: | 66,539,512 |
| Ambiguous alignments: | 284,814 |
| No feature assigned: | 7,339,032 |
| Missing chromosome in annotation: | 1,386,842 |
| Not aligned: | 3,611,665 |
Reads genomic origin
| Exonic: | 66,539,512 / 90.07% |
| Intronic: | 3,908,808 / 5.29% |
| Intergenic: | 3,430,224 / 4.64% |
| Intronic/intergenic overlapping exon: | 3,476,577 / 4.71% |
Transcript coverage profile
| 5' bias: | 0.09 |
| 3' bias: | 0.11 |
| 5'-3' bias: | 2.41 |
Junction analysis
| Reads at junctions: | 22,236,808 |
| ACCT | 5.95% |
| TCCT | 5.73% |
| ATCT | 4.79% |
| AGGT | 3.87% |
| CCCT | 3.61% |
| AGGA | 2.78% |
| TCCC | 2.76% |
| GCCT | 2.61% |
| CGTA | 2.45% |
| AGGC | 2.24% |
| CCCA | 2.12% |

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