Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:03:13 GMT 2023 |
| BAM file: | SRX7354247.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): | 38,363,422 / 38,313,731 |
| Number of aligned pairs (without duplicates): | 38,305,241 |
| Total number of alignments: | 81,450,009 |
| Number of secondary alignments: | 4,772,856 |
| Number of non-unique alignments: | 7,782,762 |
| Aligned to genes: | 62,118,412 |
| Ambiguous alignments: | 205,160 |
| No feature assigned: | 10,952,328 |
| Missing chromosome in annotation: | 391,347 |
| Not aligned: | 3,673,401 |
Reads genomic origin
| Exonic: | 62,118,412 / 85.01% |
| Intronic: | 7,708,056 / 10.55% |
| Intergenic: | 3,244,272 / 4.44% |
| Intronic/intergenic overlapping exon: | 2,985,252 / 4.09% |
Transcript coverage profile
| 5' bias: | 0.44 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 21,511,206 |
| ACCT | 5.34% |
| AGGT | 4.72% |
| ATCT | 3.81% |
| AGGA | 3.64% |
| GCCT | 3.35% |
| TCCT | 3.27% |
| AGCT | 2.68% |
| CCCT | 2.59% |
| AGGC | 2.36% |
| AGAT | 2.36% |
| TTCT | 2.15% |
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