Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:59:17 GMT 2023 |
| BAM file: | SRX7354353.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): | 34,792,685 / 34,780,285 |
| Number of aligned pairs (without duplicates): | 34,777,503 |
| Total number of alignments: | 74,629,900 |
| Number of secondary alignments: | 5,056,930 |
| Number of non-unique alignments: | 8,265,686 |
| Aligned to genes: | 54,592,633 |
| Ambiguous alignments: | 200,522 |
| No feature assigned: | 11,193,028 |
| Missing chromosome in annotation: | 378,031 |
| Not aligned: | 2,305,876 |
Reads genomic origin
| Exonic: | 54,592,633 / 82.99% |
| Intronic: | 6,925,938 / 10.53% |
| Intergenic: | 4,267,090 / 6.49% |
| Intronic/intergenic overlapping exon: | 2,187,974 / 3.33% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.26 |
| 5'-3' bias: | 1.65 |
Junction analysis
| Reads at junctions: | 19,035,250 |
| ACCT | 5.21% |
| AGGT | 4.77% |
| ATCT | 3.57% |
| TCCT | 3.51% |
| AGGA | 3.46% |
| GCCT | 3.13% |
| AGCT | 2.64% |
| CCCT | 2.56% |
| AGGC | 2.43% |
| TTCT | 2.29% |
| AGAT | 2.21% |
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