Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:43:52 GMT 2023 |
| BAM file: | SRX7354299.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): | 44,125,859 / 44,088,221 |
| Number of aligned pairs (without duplicates): | 44,083,363 |
| Total number of alignments: | 93,816,858 |
| Number of secondary alignments: | 5,602,778 |
| Number of non-unique alignments: | 8,541,249 |
| Aligned to genes: | 70,384,529 |
| Ambiguous alignments: | 257,424 |
| No feature assigned: | 13,836,430 |
| Missing chromosome in annotation: | 797,226 |
| Not aligned: | 5,094,696 |
Reads genomic origin
| Exonic: | 70,384,529 / 83.57% |
| Intronic: | 8,783,178 / 10.43% |
| Intergenic: | 5,053,252 / 6% |
| Intronic/intergenic overlapping exon: | 3,431,241 / 4.07% |
Transcript coverage profile
| 5' bias: | 0.51 |
| 3' bias: | 0.26 |
| 5'-3' bias: | 1.82 |
Junction analysis
| Reads at junctions: | 28,672,667 |
| ACCT | 5.32% |
| AGGT | 4.55% |
| GCCT | 3.68% |
| ATCT | 3.53% |
| TCCT | 3.45% |
| AGGA | 3.33% |
| AGCT | 2.79% |
| CCCT | 2.68% |
| AGGC | 2.42% |
| TTCT | 2.3% |
| AGAT | 2.1% |
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