Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:28:07 GMT 2023 |
| BAM file: | SRX7354289.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): | 52,631,495 / 52,605,509 |
| Number of aligned pairs (without duplicates): | 52,594,053 |
| Total number of alignments: | 113,718,970 |
| Number of secondary alignments: | 8,481,966 |
| Number of non-unique alignments: | 13,419,243 |
| Aligned to genes: | 90,554,612 |
| Ambiguous alignments: | 393,234 |
| No feature assigned: | 8,391,253 |
| Missing chromosome in annotation: | 960,628 |
| Not aligned: | 2,217,064 |
Reads genomic origin
| Exonic: | 90,554,612 / 91.52% |
| Intronic: | 4,241,051 / 4.29% |
| Intergenic: | 4,150,202 / 4.19% |
| Intronic/intergenic overlapping exon: | 3,535,554 / 3.57% |
Transcript coverage profile
| 5' bias: | 0.1 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 2.06 |
Junction analysis
| Reads at junctions: | 23,820,891 |
| ACCT | 4.85% |
| AGGT | 4.59% |
| TCCT | 4.41% |
| ATCT | 4.22% |
| CCCT | 3.47% |
| AGGA | 3.32% |
| AGGC | 2.36% |
| AGCT | 2.13% |
| GCCT | 2.13% |
| TTCT | 1.97% |
| AGAC | 1.84% |
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