Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:28:41 GMT 2023 |
| BAM file: | SRX7354199.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): | 68,191,728 / 68,112,484 |
| Number of aligned pairs (without duplicates): | 68,089,603 |
| Total number of alignments: | 149,085,688 |
| Number of secondary alignments: | 12,781,476 |
| Number of non-unique alignments: | 19,188,447 |
| Aligned to genes: | 116,356,982 |
| Ambiguous alignments: | 499,705 |
| No feature assigned: | 11,132,710 |
| Missing chromosome in annotation: | 1,907,844 |
| Not aligned: | 11,338,136 |
Reads genomic origin
| Exonic: | 116,356,982 / 91.27% |
| Intronic: | 5,748,148 / 4.51% |
| Intergenic: | 5,384,562 / 4.22% |
| Intronic/intergenic overlapping exon: | 5,103,313 / 4% |
Transcript coverage profile
| 5' bias: | 0.14 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 2.26 |
Junction analysis
| Reads at junctions: | 37,028,457 |
| TCCT | 4.71% |
| ACCT | 4.57% |
| AGGT | 4.49% |
| ATCT | 4.36% |
| CCCT | 3.88% |
| AGGA | 3.15% |
| AGGC | 2.55% |
| AGAC | 2.41% |
| GCCT | 2.14% |
| AGCT | 2.1% |
| GTCT | 1.95% |
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