Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:14:48 GMT 2023 |
| BAM file: | SRX7354170.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): | 24,267,084 / 24,253,501 |
| Number of aligned pairs (without duplicates): | 24,249,879 |
| Total number of alignments: | 52,226,663 |
| Number of secondary alignments: | 3,706,078 |
| Number of non-unique alignments: | 6,342,544 |
| Aligned to genes: | 39,523,490 |
| Ambiguous alignments: | 98,501 |
| No feature assigned: | 6,036,550 |
| Missing chromosome in annotation: | 225,578 |
| Not aligned: | 1,365,875 |
Reads genomic origin
| Exonic: | 39,523,490 / 86.75% |
| Intronic: | 3,354,052 / 7.36% |
| Intergenic: | 2,682,498 / 5.89% |
| Intronic/intergenic overlapping exon: | 1,777,156 / 3.9% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 2.35 |
Junction analysis
| Reads at junctions: | 8,078,529 |
| ACCT | 5.25% |
| AGGT | 4.62% |
| ATCT | 3.64% |
| AGGA | 3.51% |
| TCCT | 3.4% |
| GCCT | 3.26% |
| AGCT | 2.64% |
| TTCT | 2.39% |
| CCCT | 2.31% |
| AGGC | 2.24% |
| AGAT | 2.19% |
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