Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:00:20 GMT 2023 |
| BAM file: | SRX7354268.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): | 45,214,002 / 45,187,637 |
| Number of aligned pairs (without duplicates): | 45,177,618 |
| Total number of alignments: | 97,759,854 |
| Number of secondary alignments: | 7,358,215 |
| Number of non-unique alignments: | 11,464,691 |
| Aligned to genes: | 77,796,320 |
| Ambiguous alignments: | 363,721 |
| No feature assigned: | 7,356,290 |
| Missing chromosome in annotation: | 778,832 |
| Not aligned: | 3,522,613 |
Reads genomic origin
| Exonic: | 77,796,320 / 91.36% |
| Intronic: | 4,482,980 / 5.26% |
| Intergenic: | 2,873,310 / 3.37% |
| Intronic/intergenic overlapping exon: | 3,633,591 / 4.27% |
Transcript coverage profile
| 5' bias: | 0.12 |
| 3' bias: | 0.11 |
| 5'-3' bias: | 2.47 |
Junction analysis
| Reads at junctions: | 27,231,485 |
| ACCT | 5.11% |
| TCCT | 4.77% |
| AGGT | 4.66% |
| ATCT | 4.37% |
| AGGA | 3% |
| CCCT | 2.89% |
| AGGC | 2.65% |
| GCCT | 2.11% |
| AGAC | 2.07% |
| AGCT | 2.02% |
| AGAA | 1.72% |
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