Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:21:25 GMT 2023 |
| BAM file: | SRX7354391.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): | 40,672,443 / 40,633,648 |
| Number of aligned pairs (without duplicates): | 40,629,590 |
| Total number of alignments: | 86,572,214 |
| Number of secondary alignments: | 5,266,123 |
| Number of non-unique alignments: | 8,869,574 |
| Aligned to genes: | 66,829,164 |
| Ambiguous alignments: | 223,123 |
| No feature assigned: | 10,346,323 |
| Missing chromosome in annotation: | 304,030 |
| Not aligned: | 3,911,155 |
Reads genomic origin
| Exonic: | 66,829,164 / 86.59% |
| Intronic: | 6,700,508 / 8.68% |
| Intergenic: | 3,645,815 / 4.72% |
| Intronic/intergenic overlapping exon: | 2,555,439 / 3.31% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.92 |
Junction analysis
| Reads at junctions: | 20,668,773 |
| ACCT | 5.42% |
| AGGT | 4.57% |
| ATCT | 3.65% |
| AGGA | 3.49% |
| TCCT | 3.46% |
| GCCT | 3.4% |
| AGCT | 2.7% |
| CCCT | 2.36% |
| AGGC | 2.34% |
| AGAT | 2.21% |
| TTCT | 2.11% |
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