Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:16:33 GMT 2023 |
| BAM file: | SRX7354384.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): | 56,137,570 / 56,076,345 |
| Number of aligned pairs (without duplicates): | 56,069,686 |
| Total number of alignments: | 122,057,020 |
| Number of secondary alignments: | 9,843,105 |
| Number of non-unique alignments: | 16,731,113 |
| Aligned to genes: | 94,862,845 |
| Ambiguous alignments: | 299,716 |
| No feature assigned: | 9,490,222 |
| Missing chromosome in annotation: | 673,124 |
| Not aligned: | 5,289,045 |
Reads genomic origin
| Exonic: | 94,862,845 / 90.91% |
| Intronic: | 4,011,818 / 3.84% |
| Intergenic: | 5,478,404 / 5.25% |
| Intronic/intergenic overlapping exon: | 3,548,376 / 3.4% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.92 |
Junction analysis
| Reads at junctions: | 26,780,016 |
| ACCT | 5.39% |
| AGGT | 4.46% |
| TCCT | 3.85% |
| ATCT | 3.78% |
| AGGA | 3.38% |
| GCCT | 3.2% |
| CCCT | 2.46% |
| AGCT | 2.38% |
| AGGC | 2.26% |
| TTCT | 2.26% |
| AGAT | 1.96% |

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