Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:00:54 GMT 2023 |
| BAM file: | SRX7354286.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): | 50,804,449 / 50,767,969 |
| Number of aligned pairs (without duplicates): | 50,749,427 |
| Total number of alignments: | 110,041,040 |
| Number of secondary alignments: | 8,468,622 |
| Number of non-unique alignments: | 13,310,122 |
| Aligned to genes: | 87,019,877 |
| Ambiguous alignments: | 300,344 |
| No feature assigned: | 8,473,427 |
| Missing chromosome in annotation: | 937,270 |
| Not aligned: | 4,721,272 |
Reads genomic origin
| Exonic: | 87,019,877 / 91.13% |
| Intronic: | 4,601,633 / 4.82% |
| Intergenic: | 3,871,794 / 4.05% |
| Intronic/intergenic overlapping exon: | 3,835,860 / 4.02% |
Transcript coverage profile
| 5' bias: | 0.1 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 1.89 |
Junction analysis
| Reads at junctions: | 25,639,743 |
| ACCT | 5.65% |
| TCCT | 4.87% |
| ATCT | 4.76% |
| AGGT | 4.1% |
| CCCT | 3.14% |
| GCCT | 2.86% |
| AGGA | 2.83% |
| TCCC | 2.5% |
| AGGC | 2.21% |
| CGTA | 2.07% |
| CCCA | 1.98% |
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