Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:32:07 GMT 2023 |
| BAM file: | SRX7354159.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): | 42,291,419 / 42,204,373 |
| Number of aligned pairs (without duplicates): | 42,193,568 |
| Total number of alignments: | 91,808,775 |
| Number of secondary alignments: | 7,312,983 |
| Number of non-unique alignments: | 10,951,641 |
| Aligned to genes: | 71,391,544 |
| Ambiguous alignments: | 314,096 |
| No feature assigned: | 8,080,574 |
| Missing chromosome in annotation: | 1,070,920 |
| Not aligned: | 10,989,214 |
Reads genomic origin
| Exonic: | 71,391,544 / 89.83% |
| Intronic: | 4,658,783 / 5.86% |
| Intergenic: | 3,421,791 / 4.31% |
| Intronic/intergenic overlapping exon: | 3,937,813 / 4.95% |
Transcript coverage profile
| 5' bias: | 0.1 |
| 3' bias: | 0.1 |
| 5'-3' bias: | 2.32 |
Junction analysis
| Reads at junctions: | 22,436,340 |
| TCCT | 6.03% |
| ACCT | 5.48% |
| ATCT | 4.83% |
| CCCT | 3.92% |
| AGGT | 3.88% |
| AGGA | 2.72% |
| GCCT | 2.31% |
| TCCC | 2.27% |
| AGGC | 2.22% |
| GTCT | 2.14% |
| TTCT | 1.94% |
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