Input data and parameters
Input
| Analysis date: | Tue Oct 31 17:30:30 GMT 2023 |
| BAM file: | SRX7354410.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): | 32,362,823 / 32,343,261 |
| Number of aligned pairs (without duplicates): | 32,340,369 |
| Total number of alignments: | 68,535,463 |
| Number of secondary alignments: | 3,829,379 |
| Number of non-unique alignments: | 6,275,514 |
| Aligned to genes: | 54,063,854 |
| Ambiguous alignments: | 186,998 |
| No feature assigned: | 7,689,163 |
| Missing chromosome in annotation: | 319,934 |
| Not aligned: | 2,331,184 |
Reads genomic origin
| Exonic: | 54,063,854 / 87.55% |
| Intronic: | 5,419,613 / 8.78% |
| Intergenic: | 2,269,550 / 3.68% |
| Intronic/intergenic overlapping exon: | 2,085,065 / 3.38% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.9 |
Junction analysis
| Reads at junctions: | 17,123,116 |
| ACCT | 5.45% |
| AGGT | 4.62% |
| ATCT | 3.54% |
| TCCT | 3.47% |
| AGGA | 3.45% |
| GCCT | 3.33% |
| AGCT | 2.72% |
| CCCT | 2.45% |
| AGGC | 2.38% |
| AGAT | 2.22% |
| TTCT | 2.09% |
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