Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:54:29 GMT 2023 |
| BAM file: | SRX7354357.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): | 34,524,482 / 34,500,902 |
| Number of aligned pairs (without duplicates): | 34,497,837 |
| Total number of alignments: | 73,362,690 |
| Number of secondary alignments: | 4,337,306 |
| Number of non-unique alignments: | 7,289,346 |
| Aligned to genes: | 58,226,690 |
| Ambiguous alignments: | 206,409 |
| No feature assigned: | 7,407,042 |
| Missing chromosome in annotation: | 233,203 |
| Not aligned: | 3,289,952 |
Reads genomic origin
| Exonic: | 58,226,690 / 88.71% |
| Intronic: | 5,314,185 / 8.1% |
| Intergenic: | 2,092,857 / 3.19% |
| Intronic/intergenic overlapping exon: | 2,015,350 / 3.07% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.05 |
Junction analysis
| Reads at junctions: | 19,632,082 |
| ACCT | 5.34% |
| AGGT | 4.69% |
| ATCT | 3.64% |
| AGGA | 3.57% |
| TCCT | 3.44% |
| GCCT | 3.1% |
| AGCT | 2.79% |
| AGGC | 2.33% |
| AGAT | 2.29% |
| CCCT | 2.27% |
| TTCT | 2.18% |
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