Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:07:16 GMT 2023 |
| BAM file: | SRX7354241.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): | 42,597,475 / 42,560,026 |
| Number of aligned pairs (without duplicates): | 42,546,347 |
| Total number of alignments: | 92,455,458 |
| Number of secondary alignments: | 7,297,957 |
| Number of non-unique alignments: | 12,056,572 |
| Aligned to genes: | 72,876,762 |
| Ambiguous alignments: | 257,677 |
| No feature assigned: | 6,720,863 |
| Missing chromosome in annotation: | 543,584 |
| Not aligned: | 4,287,993 |
Reads genomic origin
| Exonic: | 72,876,762 / 91.56% |
| Intronic: | 3,984,833 / 5.01% |
| Intergenic: | 2,736,030 / 3.44% |
| Intronic/intergenic overlapping exon: | 3,231,059 / 4.06% |
Transcript coverage profile
| 5' bias: | 0.15 |
| 3' bias: | 0.12 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 22,680,192 |
| AGGT | 5.24% |
| ACCT | 4.95% |
| TCCT | 3.9% |
| AGGA | 3.57% |
| ATCT | 3.51% |
| CCCT | 2.64% |
| AGGC | 2.52% |
| AGCT | 2.15% |
| TTCT | 2.1% |
| AGAA | 2.05% |
| GCCT | 2.03% |
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