Input data and parameters
Input
| Analysis date: | Tue Oct 31 13:23:43 GMT 2023 |
| BAM file: | SRX7354186.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): | 36,981,862 / 36,963,434 |
| Number of aligned pairs (without duplicates): | 36,960,146 |
| Total number of alignments: | 78,337,454 |
| Number of secondary alignments: | 4,392,158 |
| Number of non-unique alignments: | 7,327,110 |
| Aligned to genes: | 63,624,762 |
| Ambiguous alignments: | 230,641 |
| No feature assigned: | 6,862,128 |
| Missing chromosome in annotation: | 292,813 |
| Not aligned: | 4,665,224 |
Reads genomic origin
| Exonic: | 63,624,762 / 90.26% |
| Intronic: | 4,222,133 / 5.99% |
| Intergenic: | 2,639,995 / 3.75% |
| Intronic/intergenic overlapping exon: | 2,305,691 / 3.27% |
Transcript coverage profile
| 5' bias: | 0.24 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 21,008,843 |
| ACCT | 5.67% |
| AGGT | 4.6% |
| ATCT | 3.76% |
| TCCT | 3.59% |
| GCCT | 3.35% |
| AGGA | 3.3% |
| AGCT | 2.58% |
| CCCT | 2.35% |
| AGGC | 2.33% |
| TTCT | 2.06% |
| AGAT | 2.03% |
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