Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:09:52 GMT 2023 |
| BAM file: | SRX7354219.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): | 35,843,790 / 35,808,883 |
| Number of aligned pairs (without duplicates): | 35,806,050 |
| Total number of alignments: | 76,160,667 |
| Number of secondary alignments: | 4,507,994 |
| Number of non-unique alignments: | 7,803,299 |
| Aligned to genes: | 60,317,768 |
| Ambiguous alignments: | 154,636 |
| No feature assigned: | 7,645,883 |
| Missing chromosome in annotation: | 239,081 |
| Not aligned: | 4,645,325 |
Reads genomic origin
| Exonic: | 60,317,768 / 88.75% |
| Intronic: | 3,749,416 / 5.52% |
| Intergenic: | 3,896,467 / 5.73% |
| Intronic/intergenic overlapping exon: | 2,256,248 / 3.32% |
Transcript coverage profile
| 5' bias: | 0.19 |
| 3' bias: | 0.09 |
| 5'-3' bias: | 1.94 |
Junction analysis
| Reads at junctions: | 15,952,093 |
| ACCT | 4.87% |
| AGGT | 4.66% |
| AGGA | 3.77% |
| ATCT | 3.7% |
| TCCT | 3.34% |
| AGCT | 2.8% |
| GCCT | 2.76% |
| AGAT | 2.59% |
| TTCT | 2.39% |
| AGGC | 2.34% |
| CCCT | 2.2% |
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