Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:53:20 GMT 2023 |
| BAM file: | SRX7354115.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): | 29,838,298 / 29,818,055 |
| Number of aligned pairs (without duplicates): | 29,814,529 |
| Total number of alignments: | 63,476,624 |
| Number of secondary alignments: | 3,820,271 |
| Number of non-unique alignments: | 6,156,535 |
| Aligned to genes: | 47,510,332 |
| Ambiguous alignments: | 198,770 |
| No feature assigned: | 9,281,809 |
| Missing chromosome in annotation: | 329,178 |
| Not aligned: | 3,143,329 |
Reads genomic origin
| Exonic: | 47,510,332 / 83.66% |
| Intronic: | 6,498,077 / 11.44% |
| Intergenic: | 2,783,732 / 4.9% |
| Intronic/intergenic overlapping exon: | 2,202,608 / 3.88% |
Transcript coverage profile
| 5' bias: | 0.54 |
| 3' bias: | 0.29 |
| 5'-3' bias: | 1.78 |
Junction analysis
| Reads at junctions: | 18,577,065 |
| ACCT | 5.09% |
| AGGT | 4.78% |
| AGGA | 3.48% |
| TCCT | 3.43% |
| ATCT | 3.33% |
| GCCT | 3.13% |
| AGCT | 2.83% |
| CCCT | 2.55% |
| AGGC | 2.42% |
| TTCT | 2.21% |
| AGAT | 2.19% |
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