Input data and parameters
Input
| Analysis date: | Tue Oct 31 16:17:23 GMT 2023 |
| BAM file: | SRX7354397.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): | 120,988,440 / 120,784,066 |
| Number of aligned pairs (without duplicates): | 120,756,260 |
| Total number of alignments: | 260,955,046 |
| Number of secondary alignments: | 19,182,540 |
| Number of non-unique alignments: | 32,320,132 |
| Aligned to genes: | 197,286,625 |
| Ambiguous alignments: | 678,304 |
| No feature assigned: | 29,208,659 |
| Missing chromosome in annotation: | 1,461,326 |
| Not aligned: | 11,959,526 |
Reads genomic origin
| Exonic: | 197,286,625 / 87.1% |
| Intronic: | 19,977,517 / 8.82% |
| Intergenic: | 9,231,142 / 4.08% |
| Intronic/intergenic overlapping exon: | 11,024,286 / 4.87% |
Transcript coverage profile
| 5' bias: | 0.45 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.68 |
Junction analysis
| Reads at junctions: | 65,274,198 |
| ACCT | 5.05% |
| AGGT | 4.58% |
| TCCT | 3.81% |
| ATCT | 3.74% |
| GCCT | 3.57% |
| AGGA | 3.21% |
| CCCT | 2.76% |
| AGCT | 2.73% |
| AGGC | 2.4% |
| TTCT | 2.3% |
| AGAT | 2% |
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