Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:30:07 GMT 2023 |
| BAM file: | SRX7354335.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): | 51,932,319 / 51,881,634 |
| Number of aligned pairs (without duplicates): | 51,874,937 |
| Total number of alignments: | 111,146,297 |
| Number of secondary alignments: | 7,332,344 |
| Number of non-unique alignments: | 12,347,491 |
| Aligned to genes: | 87,599,963 |
| Ambiguous alignments: | 306,042 |
| No feature assigned: | 10,429,478 |
| Missing chromosome in annotation: | 463,323 |
| Not aligned: | 14,904,677 |
Reads genomic origin
| Exonic: | 87,599,963 / 89.36% |
| Intronic: | 6,161,620 / 6.29% |
| Intergenic: | 4,267,858 / 4.35% |
| Intronic/intergenic overlapping exon: | 2,934,142 / 2.99% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.21 |
Junction analysis
| Reads at junctions: | 25,377,641 |
| ACCT | 5.51% |
| AGGT | 4.8% |
| ATCT | 3.73% |
| TCCT | 3.59% |
| AGGA | 3.52% |
| GCCT | 3.17% |
| CCCT | 2.72% |
| AGCT | 2.52% |
| AGGC | 2.37% |
| TTCT | 2.29% |
| AGAT | 2.23% |
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