Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:33:22 GMT 2023 |
| BAM file: | SRX7354301.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): | 48,518,338 / 48,502,337 |
| Number of aligned pairs (without duplicates): | 48,480,640 |
| Total number of alignments: | 107,131,429 |
| Number of secondary alignments: | 10,110,754 |
| Number of non-unique alignments: | 15,805,132 |
| Aligned to genes: | 81,848,094 |
| Ambiguous alignments: | 349,132 |
| No feature assigned: | 8,188,585 |
| Missing chromosome in annotation: | 940,486 |
| Not aligned: | 4,383,679 |
Reads genomic origin
| Exonic: | 81,848,094 / 90.91% |
| Intronic: | 4,629,773 / 5.14% |
| Intergenic: | 3,558,812 / 3.95% |
| Intronic/intergenic overlapping exon: | 4,204,894 / 4.67% |
Transcript coverage profile
| 5' bias: | 0.09 |
| 3' bias: | 0.12 |
| 5'-3' bias: | 2.02 |
Junction analysis
| Reads at junctions: | 25,541,965 |
| TCCT | 5.68% |
| ACCT | 5.68% |
| ATCT | 4.68% |
| AGGT | 4% |
| CCCT | 3.64% |
| AGGA | 2.78% |
| GCCT | 2.43% |
| AGGC | 2.28% |
| TCCC | 2.24% |
| TTCT | 2.01% |
| CGTA | 1.93% |
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