Input data and parameters
Input
| Analysis date: | Tue Oct 31 17:37:14 GMT 2023 |
| BAM file: | SRX7354412.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): | 53,141,033 / 53,105,945 |
| Number of aligned pairs (without duplicates): | 53,099,626 |
| Total number of alignments: | 113,660,721 |
| Number of secondary alignments: | 7,413,743 |
| Number of non-unique alignments: | 12,252,572 |
| Aligned to genes: | 87,299,418 |
| Ambiguous alignments: | 326,254 |
| No feature assigned: | 13,220,336 |
| Missing chromosome in annotation: | 562,141 |
| Not aligned: | 10,103,186 |
Reads genomic origin
| Exonic: | 87,299,418 / 86.85% |
| Intronic: | 8,752,604 / 8.71% |
| Intergenic: | 4,467,732 / 4.44% |
| Intronic/intergenic overlapping exon: | 3,501,089 / 3.48% |
Transcript coverage profile
| 5' bias: | 0.35 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.94 |
Junction analysis
| Reads at junctions: | 29,198,266 |
| ACCT | 5.44% |
| AGGT | 4.66% |
| ATCT | 3.66% |
| TCCT | 3.54% |
| AGGA | 3.52% |
| GCCT | 3.25% |
| AGCT | 2.63% |
| CCCT | 2.5% |
| AGGC | 2.38% |
| AGAT | 2.28% |
| TTCT | 2.28% |
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