Input data and parameters
Input
| Analysis date: | Mon Oct 30 13:15:40 GMT 2023 |
| BAM file: | SRX7354188.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): | 77,171,218 / 77,078,129 |
| Number of aligned pairs (without duplicates): | 77,071,324 |
| Total number of alignments: | 162,617,416 |
| Number of secondary alignments: | 8,368,069 |
| Number of non-unique alignments: | 13,913,559 |
| Aligned to genes: | 132,003,600 |
| Ambiguous alignments: | 377,175 |
| No feature assigned: | 15,718,235 |
| Missing chromosome in annotation: | 604,847 |
| Not aligned: | 6,855,957 |
Reads genomic origin
| Exonic: | 132,003,600 / 89.36% |
| Intronic: | 8,476,216 / 5.74% |
| Intergenic: | 7,242,019 / 4.9% |
| Intronic/intergenic overlapping exon: | 5,774,933 / 3.91% |
Transcript coverage profile
| 5' bias: | 0.41 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 2.2 |
Junction analysis
| Reads at junctions: | 45,019,235 |
| ACCT | 5.45% |
| AGGT | 4.8% |
| AGGA | 3.57% |
| ATCT | 3.48% |
| TCCT | 3.32% |
| GCCT | 3.1% |
| AGCT | 2.82% |
| AGGC | 2.43% |
| CCCT | 2.26% |
| AGAT | 2.2% |
| TTCT | 2.16% |
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