Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:44:12 GMT 2023 |
| BAM file: | SRX7354177.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): | 85,815,572 / 85,668,977 |
| Number of aligned pairs (without duplicates): | 85,661,074 |
| Total number of alignments: | 182,304,534 |
| Number of secondary alignments: | 10,819,985 |
| Number of non-unique alignments: | 15,660,330 |
| Aligned to genes: | 135,504,293 |
| Ambiguous alignments: | 482,450 |
| No feature assigned: | 28,797,845 |
| Missing chromosome in annotation: | 1,859,616 |
| Not aligned: | 6,300,089 |
Reads genomic origin
| Exonic: | 135,504,293 / 82.47% |
| Intronic: | 20,074,711 / 12.22% |
| Intergenic: | 8,723,134 / 5.31% |
| Intronic/intergenic overlapping exon: | 7,551,578 / 4.6% |
Transcript coverage profile
| 5' bias: | 0.57 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 63,886,526 |
| ACCT | 5.32% |
| AGGT | 4.72% |
| GCCT | 3.57% |
| AGGA | 3.56% |
| TCCT | 3.39% |
| ATCT | 3.37% |
| AGCT | 2.91% |
| CCCT | 2.56% |
| AGGC | 2.43% |
| AGAT | 2.3% |
| TTCT | 2.22% |
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