Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:47:59 GMT 2023 |
| BAM file: | SRX7354376.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): | 29,692,001 / 29,673,584 |
| Number of aligned pairs (without duplicates): | 29,669,824 |
| Total number of alignments: | 63,383,786 |
| Number of secondary alignments: | 4,018,201 |
| Number of non-unique alignments: | 6,524,804 |
| Aligned to genes: | 51,186,047 |
| Ambiguous alignments: | 178,441 |
| No feature assigned: | 5,140,704 |
| Missing chromosome in annotation: | 353,790 |
| Not aligned: | 2,349,751 |
Reads genomic origin
| Exonic: | 51,186,047 / 90.87% |
| Intronic: | 2,632,893 / 4.67% |
| Intergenic: | 2,507,811 / 4.45% |
| Intronic/intergenic overlapping exon: | 1,960,160 / 3.48% |
Transcript coverage profile
| 5' bias: | 0.18 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.12 |
Junction analysis
| Reads at junctions: | 14,191,689 |
| ACCT | 5.43% |
| AGGT | 4.68% |
| ATCT | 4.21% |
| TCCT | 4.14% |
| AGGA | 3.22% |
| GCCT | 2.89% |
| CCCT | 2.83% |
| TTCT | 2.32% |
| AGGC | 2.25% |
| AGCT | 2.14% |
| AGAA | 1.87% |
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