Input data and parameters
Input
| Analysis date: | Mon Oct 30 13:20:06 GMT 2023 |
| BAM file: | SRX7354209.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): | 78,289,305 / 78,247,946 |
| Number of aligned pairs (without duplicates): | 78,238,085 |
| Total number of alignments: | 167,937,749 |
| Number of secondary alignments: | 11,400,498 |
| Number of non-unique alignments: | 17,325,739 |
| Aligned to genes: | 136,880,191 |
| Ambiguous alignments: | 577,767 |
| No feature assigned: | 11,674,113 |
| Missing chromosome in annotation: | 1,479,939 |
| Not aligned: | 4,940,945 |
Reads genomic origin
| Exonic: | 136,880,191 / 92.14% |
| Intronic: | 6,782,564 / 4.57% |
| Intergenic: | 4,891,549 / 3.29% |
| Intronic/intergenic overlapping exon: | 5,312,687 / 3.58% |
Transcript coverage profile
| 5' bias: | 0.12 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.47 |
Junction analysis
| Reads at junctions: | 47,474,137 |
| ACCT | 5.22% |
| AGGT | 4.8% |
| TCCT | 4.05% |
| ATCT | 4.01% |
| CCCT | 3.22% |
| AGGA | 3.1% |
| AGGC | 2.58% |
| GCCT | 2.53% |
| AGCT | 2.12% |
| TTCT | 2.06% |
| AGAA | 1.97% |
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