Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:21:23 GMT 2023 |
| BAM file: | SRX7354149.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): | 50,378,992 / 50,325,321 |
| Number of aligned pairs (without duplicates): | 50,301,081 |
| Total number of alignments: | 107,191,100 |
| Number of secondary alignments: | 6,486,787 |
| Number of non-unique alignments: | 10,447,453 |
| Aligned to genes: | 84,572,405 |
| Ambiguous alignments: | 332,673 |
| No feature assigned: | 11,253,456 |
| Missing chromosome in annotation: | 585,113 |
| Not aligned: | 2,223,511 |
Reads genomic origin
| Exonic: | 84,572,405 / 88.26% |
| Intronic: | 7,628,894 / 7.96% |
| Intergenic: | 3,624,562 / 3.78% |
| Intronic/intergenic overlapping exon: | 4,306,595 / 4.49% |
Transcript coverage profile
| 5' bias: | 0.45 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.89 |
Junction analysis
| Reads at junctions: | 31,040,815 |
| ACCT | 5.4% |
| AGGT | 5.04% |
| AGGA | 3.55% |
| ATCT | 3.53% |
| TCCT | 3.44% |
| GCCT | 3.22% |
| AGCT | 2.68% |
| CCCT | 2.57% |
| AGGC | 2.44% |
| TTCT | 2.3% |
| AGAT | 2.2% |
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