Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:53:53 GMT 2023 |
| BAM file: | SRX7354371.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): | 38,763,882 / 38,729,948 |
| Number of aligned pairs (without duplicates): | 38,726,639 |
| Total number of alignments: | 84,718,154 |
| Number of secondary alignments: | 7,224,324 |
| Number of non-unique alignments: | 10,042,492 |
| Aligned to genes: | 64,829,228 |
| Ambiguous alignments: | 236,288 |
| No feature assigned: | 8,187,693 |
| Missing chromosome in annotation: | 1,422,453 |
| Not aligned: | 4,452,184 |
Reads genomic origin
| Exonic: | 64,829,228 / 88.79% |
| Intronic: | 5,374,012 / 7.36% |
| Intergenic: | 2,813,681 / 3.85% |
| Intronic/intergenic overlapping exon: | 2,562,872 / 3.51% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.75 |
Junction analysis
| Reads at junctions: | 20,415,271 |
| ACCT | 5.35% |
| AGGT | 4.53% |
| ATCT | 3.65% |
| TCCT | 3.53% |
| GCCT | 3.43% |
| AGGA | 3.21% |
| TTCT | 2.76% |
| CCCT | 2.67% |
| AGCT | 2.65% |
| AGGC | 2.34% |
| AGAT | 2.05% |
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