Input data and parameters
Input
| Analysis date: | Mon Oct 30 12:46:59 GMT 2023 |
| BAM file: | SRX7354212.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): | 37,942,763 / 37,933,733 |
| Number of aligned pairs (without duplicates): | 37,930,542 |
| Total number of alignments: | 80,868,024 |
| Number of secondary alignments: | 4,991,528 |
| Number of non-unique alignments: | 8,258,805 |
| Aligned to genes: | 63,934,321 |
| Ambiguous alignments: | 214,149 |
| No feature assigned: | 8,095,208 |
| Missing chromosome in annotation: | 365,541 |
| Not aligned: | 1,442,106 |
Reads genomic origin
| Exonic: | 63,934,321 / 88.76% |
| Intronic: | 5,163,269 / 7.17% |
| Intergenic: | 2,931,939 / 4.07% |
| Intronic/intergenic overlapping exon: | 2,154,000 / 2.99% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.02 |
Junction analysis
| Reads at junctions: | 19,757,900 |
| ACCT | 5.56% |
| AGGT | 4.78% |
| AGGA | 3.52% |
| ATCT | 3.49% |
| GCCT | 3.28% |
| TCCT | 3.26% |
| AGCT | 2.77% |
| AGGC | 2.41% |
| AGAT | 2.3% |
| CCCT | 2.29% |
| TTCT | 2.17% |

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