Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:25:27 GMT 2023 |
| BAM file: | SRX7354111.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): | 42,412,643 / 42,348,916 |
| Number of aligned pairs (without duplicates): | 42,330,798 |
| Total number of alignments: | 89,880,843 |
| Number of secondary alignments: | 5,119,284 |
| Number of non-unique alignments: | 8,634,169 |
| Aligned to genes: | 69,555,711 |
| Ambiguous alignments: | 203,488 |
| No feature assigned: | 11,161,044 |
| Missing chromosome in annotation: | 326,431 |
| Not aligned: | 8,982,627 |
Reads genomic origin
| Exonic: | 69,555,711 / 86.17% |
| Intronic: | 7,213,353 / 8.94% |
| Intergenic: | 3,947,691 / 4.89% |
| Intronic/intergenic overlapping exon: | 3,015,251 / 3.74% |
Transcript coverage profile
| 5' bias: | 0.24 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.09 |
Junction analysis
| Reads at junctions: | 18,322,302 |
| ACCT | 5.32% |
| AGGT | 4.73% |
| ATCT | 3.79% |
| AGGA | 3.61% |
| TCCT | 3.48% |
| GCCT | 2.89% |
| AGCT | 2.64% |
| AGAT | 2.47% |
| CCCT | 2.44% |
| AGGC | 2.42% |
| TTCT | 2.21% |
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