Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:38:59 GMT 2023 |
| BAM file: | SRX7354207.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): | 42,232,833 / 42,208,619 |
| Number of aligned pairs (without duplicates): | 42,200,447 |
| Total number of alignments: | 89,788,179 |
| Number of secondary alignments: | 5,346,727 |
| Number of non-unique alignments: | 8,264,363 |
| Aligned to genes: | 69,071,347 |
| Ambiguous alignments: | 236,738 |
| No feature assigned: | 11,547,647 |
| Missing chromosome in annotation: | 668,084 |
| Not aligned: | 2,097,226 |
Reads genomic origin
| Exonic: | 69,071,347 / 85.68% |
| Intronic: | 8,224,162 / 10.2% |
| Intergenic: | 3,323,485 / 4.12% |
| Intronic/intergenic overlapping exon: | 3,245,592 / 4.03% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.07 |
Junction analysis
| Reads at junctions: | 22,830,658 |
| ACCT | 5.41% |
| AGGT | 4.78% |
| AGGA | 3.57% |
| ATCT | 3.53% |
| GCCT | 3.32% |
| TCCT | 3.29% |
| AGCT | 2.7% |
| AGGC | 2.42% |
| CCCT | 2.33% |
| AGAT | 2.29% |
| TTCT | 2.13% |
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