Input data and parameters
Input
| Analysis date: | Mon Oct 30 12:47:21 GMT 2023 |
| BAM file: | SRX7354201.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): | 29,560,511 / 29,543,548 |
| Number of aligned pairs (without duplicates): | 29,540,619 |
| Total number of alignments: | 62,870,923 |
| Number of secondary alignments: | 3,766,864 |
| Number of non-unique alignments: | 6,136,730 |
| Aligned to genes: | 49,910,603 |
| Ambiguous alignments: | 180,739 |
| No feature assigned: | 6,304,607 |
| Missing chromosome in annotation: | 338,244 |
| Not aligned: | 3,592,527 |
Reads genomic origin
| Exonic: | 49,910,603 / 88.78% |
| Intronic: | 4,244,244 / 7.55% |
| Intergenic: | 2,060,363 / 3.67% |
| Intronic/intergenic overlapping exon: | 1,752,121 / 3.12% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.94 |
Junction analysis
| Reads at junctions: | 15,431,333 |
| ACCT | 5.38% |
| AGGT | 4.72% |
| AGGA | 3.55% |
| ATCT | 3.53% |
| TCCT | 3.51% |
| GCCT | 3.22% |
| AGCT | 2.71% |
| CCCT | 2.48% |
| AGGC | 2.38% |
| AGAT | 2.21% |
| TTCT | 2.09% |
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