Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:31:18 GMT 2023 |
| BAM file: | SRX7354184.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): | 46,340,904 / 46,317,068 |
| Number of aligned pairs (without duplicates): | 46,309,534 |
| Total number of alignments: | 100,184,925 |
| Number of secondary alignments: | 7,526,953 |
| Number of non-unique alignments: | 11,602,696 |
| Aligned to genes: | 79,715,103 |
| Ambiguous alignments: | 360,075 |
| No feature assigned: | 7,612,390 |
| Missing chromosome in annotation: | 894,661 |
| Not aligned: | 3,279,928 |
Reads genomic origin
| Exonic: | 79,715,103 / 91.28% |
| Intronic: | 4,113,998 / 4.71% |
| Intergenic: | 3,498,392 / 4.01% |
| Intronic/intergenic overlapping exon: | 3,713,368 / 4.25% |
Transcript coverage profile
| 5' bias: | 0.13 |
| 3' bias: | 0.12 |
| 5'-3' bias: | 2.33 |
Junction analysis
| Reads at junctions: | 27,180,805 |
| ACCT | 5.3% |
| AGGT | 4.67% |
| ATCT | 4.52% |
| TCCT | 4.24% |
| CCCT | 3.34% |
| AGGA | 2.73% |
| AGGC | 2.69% |
| AGAC | 2.39% |
| GCCT | 2.34% |
| AGCT | 2.02% |
| TTCT | 1.9% |
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