Input data and parameters
Input
| Analysis date: | Mon Oct 30 12:49:47 GMT 2023 |
| BAM file: | SRX7354234.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): | 38,927,039 / 38,897,006 |
| Number of aligned pairs (without duplicates): | 38,892,981 |
| Total number of alignments: | 82,110,446 |
| Number of secondary alignments: | 4,286,401 |
| Number of non-unique alignments: | 7,199,834 |
| Aligned to genes: | 67,195,445 |
| Ambiguous alignments: | 217,100 |
| No feature assigned: | 7,211,262 |
| Missing chromosome in annotation: | 286,805 |
| Not aligned: | 3,915,797 |
Reads genomic origin
| Exonic: | 67,195,445 / 90.31% |
| Intronic: | 4,019,375 / 5.4% |
| Intergenic: | 3,191,887 / 4.29% |
| Intronic/intergenic overlapping exon: | 2,723,126 / 3.66% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.2 |
Junction analysis
| Reads at junctions: | 22,465,272 |
| ACCT | 5.5% |
| AGGT | 4.78% |
| AGGA | 3.56% |
| ATCT | 3.48% |
| TCCT | 3.39% |
| GCCT | 3.22% |
| AGCT | 2.68% |
| AGGC | 2.46% |
| AGAT | 2.32% |
| CCCT | 2.27% |
| TTCT | 2.1% |
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