Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:22:02 GMT 2023 |
| BAM file: | SRX7354276.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): | 47,724,956 / 47,487,891 |
| Number of aligned pairs (without duplicates): | 47,449,698 |
| Total number of alignments: | 113,422,231 |
| Number of secondary alignments: | 18,209,384 |
| Number of non-unique alignments: | 16,834,182 |
| Aligned to genes: | 67,603,730 |
| Ambiguous alignments: | 225,244 |
| No feature assigned: | 21,076,458 |
| Missing chromosome in annotation: | 7,682,617 |
| Not aligned: | 24,589,517 |
Reads genomic origin
| Exonic: | 67,603,730 / 76.23% |
| Intronic: | 11,272,500 / 12.71% |
| Intergenic: | 9,803,958 / 11.06% |
| Intronic/intergenic overlapping exon: | 4,394,135 / 4.96% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.76 |
Junction analysis
| Reads at junctions: | 22,132,105 |
| ACCT | 5.14% |
| AGGT | 4.68% |
| ATCT | 3.6% |
| TCCT | 3.53% |
| AGGA | 3.37% |
| GCCT | 3.29% |
| AGCT | 2.72% |
| CCCT | 2.58% |
| AGGC | 2.39% |
| TTCT | 2.26% |
| AGAT | 2.15% |
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