Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:44:23 GMT 2023 |
| BAM file: | SRX7354240.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): | 69,451,997 / 69,319,447 |
| Number of aligned pairs (without duplicates): | 69,309,176 |
| Total number of alignments: | 146,825,075 |
| Number of secondary alignments: | 8,053,631 |
| Number of non-unique alignments: | 12,740,779 |
| Aligned to genes: | 112,059,113 |
| Ambiguous alignments: | 432,309 |
| No feature assigned: | 20,739,164 |
| Missing chromosome in annotation: | 853,710 |
| Not aligned: | 15,621,688 |
Reads genomic origin
| Exonic: | 112,059,113 / 84.38% |
| Intronic: | 14,482,353 / 10.91% |
| Intergenic: | 6,256,811 / 4.71% |
| Intronic/intergenic overlapping exon: | 5,657,534 / 4.26% |
Transcript coverage profile
| 5' bias: | 0.41 |
| 3' bias: | 0.29 |
| 5'-3' bias: | 1.67 |
Junction analysis
| Reads at junctions: | 47,595,351 |
| ACCT | 5.25% |
| AGGT | 4.7% |
| TCCT | 3.52% |
| GCCT | 3.48% |
| ATCT | 3.44% |
| AGGA | 3.32% |
| AGCT | 2.82% |
| CCCT | 2.62% |
| AGGC | 2.46% |
| TTCT | 2.2% |
| AGAT | 2.13% |
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