Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:15:13 GMT 2023 |
| BAM file: | SRX7354348.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): | 72,536,996 / 72,475,033 |
| Number of aligned pairs (without duplicates): | 72,468,922 |
| Total number of alignments: | 154,136,693 |
| Number of secondary alignments: | 9,124,664 |
| Number of non-unique alignments: | 15,150,620 |
| Aligned to genes: | 122,359,663 |
| Ambiguous alignments: | 377,440 |
| No feature assigned: | 15,540,563 |
| Missing chromosome in annotation: | 708,407 |
| Not aligned: | 10,643,469 |
Reads genomic origin
| Exonic: | 122,359,663 / 88.73% |
| Intronic: | 9,386,149 / 6.81% |
| Intergenic: | 6,154,414 / 4.46% |
| Intronic/intergenic overlapping exon: | 4,630,179 / 3.36% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 37,620,799 |
| ACCT | 5.35% |
| AGGT | 4.72% |
| ATCT | 3.86% |
| AGGA | 3.63% |
| TCCT | 3.37% |
| GCCT | 3.26% |
| AGCT | 2.72% |
| CCCT | 2.43% |
| AGGC | 2.38% |
| AGAT | 2.26% |
| TTCT | 2.24% |
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