Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:00:58 GMT 2023 |
| BAM file: | SRX7354254.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): | 20,470,536 / 20,459,383 |
| Number of aligned pairs (without duplicates): | 20,451,092 |
| Total number of alignments: | 44,328,505 |
| Number of secondary alignments: | 3,398,586 |
| Number of non-unique alignments: | 5,389,091 |
| Aligned to genes: | 34,901,129 |
| Ambiguous alignments: | 128,952 |
| No feature assigned: | 3,548,316 |
| Missing chromosome in annotation: | 361,017 |
| Not aligned: | 1,762,095 |
Reads genomic origin
| Exonic: | 34,901,129 / 90.77% |
| Intronic: | 1,761,391 / 4.58% |
| Intergenic: | 1,786,925 / 4.65% |
| Intronic/intergenic overlapping exon: | 1,580,357 / 4.11% |
Transcript coverage profile
| 5' bias: | 0.12 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 2.26 |
Junction analysis
| Reads at junctions: | 10,648,434 |
| ACCT | 5.66% |
| TCCT | 4.94% |
| ATCT | 4.39% |
| AGGT | 4.31% |
| CCCT | 2.96% |
| AGGA | 2.89% |
| GCCT | 2.73% |
| TCCC | 2.44% |
| AGGC | 2.26% |
| TTCT | 1.98% |
| AGCT | 1.93% |
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