Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:22:34 GMT 2023 |
| BAM file: | SRX7354298.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): | 44,751,398 / 44,657,302 |
| Number of aligned pairs (without duplicates): | 44,641,371 |
| Total number of alignments: | 108,284,313 |
| Number of secondary alignments: | 18,875,613 |
| Number of non-unique alignments: | 17,339,374 |
| Aligned to genes: | 63,286,447 |
| Ambiguous alignments: | 233,614 |
| No feature assigned: | 19,445,592 |
| Missing chromosome in annotation: | 7,979,286 |
| Not aligned: | 15,271,464 |
Reads genomic origin
| Exonic: | 63,286,447 / 76.5% |
| Intronic: | 10,538,203 / 12.74% |
| Intergenic: | 8,907,389 / 10.77% |
| Intronic/intergenic overlapping exon: | 4,041,550 / 4.89% |
Transcript coverage profile
| 5' bias: | 0.46 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.05 |
Junction analysis
| Reads at junctions: | 27,861,612 |
| ACCT | 5.21% |
| AGGT | 4.51% |
| GCCT | 3.52% |
| ATCT | 3.42% |
| AGGA | 3.33% |
| TCCT | 3.33% |
| AGCT | 2.78% |
| CCCT | 2.51% |
| TTCT | 2.37% |
| AGGC | 2.35% |
| AGAT | 2.13% |
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