Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:47:38 GMT 2023 |
| BAM file: | SRX7354375.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): | 33,010,145 / 32,958,052 |
| Number of aligned pairs (without duplicates): | 32,952,477 |
| Total number of alignments: | 70,343,994 |
| Number of secondary alignments: | 4,375,797 |
| Number of non-unique alignments: | 7,131,501 |
| Aligned to genes: | 53,019,891 |
| Ambiguous alignments: | 199,840 |
| No feature assigned: | 9,655,653 |
| Missing chromosome in annotation: | 337,109 |
| Not aligned: | 4,806,065 |
Reads genomic origin
| Exonic: | 53,019,891 / 84.59% |
| Intronic: | 5,685,968 / 9.07% |
| Intergenic: | 3,969,685 / 6.33% |
| Intronic/intergenic overlapping exon: | 2,229,052 / 3.56% |
Transcript coverage profile
| 5' bias: | 0.43 |
| 3' bias: | 0.3 |
| 5'-3' bias: | 1.65 |
Junction analysis
| Reads at junctions: | 20,300,477 |
| ACCT | 5.21% |
| AGGT | 4.8% |
| TCCT | 3.64% |
| AGGA | 3.45% |
| ATCT | 3.44% |
| GCCT | 3.06% |
| AGCT | 2.68% |
| CCCT | 2.47% |
| AGGC | 2.41% |
| AGAT | 2.14% |
| TTCT | 2.06% |
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