Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:03:42 GMT 2023 |
| BAM file: | SRX7354067.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): | 29,642,191 / 29,621,753 |
| Number of aligned pairs (without duplicates): | 29,619,433 |
| Total number of alignments: | 63,408,166 |
| Number of secondary alignments: | 4,144,222 |
| Number of non-unique alignments: | 6,855,660 |
| Aligned to genes: | 49,777,067 |
| Ambiguous alignments: | 178,089 |
| No feature assigned: | 6,300,637 |
| Missing chromosome in annotation: | 296,713 |
| Not aligned: | 2,359,404 |
Reads genomic origin
| Exonic: | 49,777,067 / 88.76% |
| Intronic: | 4,290,219 / 7.65% |
| Intergenic: | 2,010,418 / 3.59% |
| Intronic/intergenic overlapping exon: | 1,708,140 / 3.05% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 1.83 |
Junction analysis
| Reads at junctions: | 17,116,733 |
| ACCT | 5.55% |
| AGGT | 4.48% |
| ATCT | 3.63% |
| GCCT | 3.59% |
| TCCT | 3.44% |
| AGGA | 3.33% |
| AGCT | 2.7% |
| CCCT | 2.5% |
| AGGC | 2.37% |
| TTCT | 2.21% |
| AGAT | 2.08% |
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