Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:26:34 GMT 2023 |
| BAM file: | SRX7354134.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): | 37,391,266 / 37,365,278 |
| Number of aligned pairs (without duplicates): | 37,360,422 |
| Total number of alignments: | 79,527,199 |
| Number of secondary alignments: | 4,770,655 |
| Number of non-unique alignments: | 8,240,486 |
| Aligned to genes: | 62,097,508 |
| Ambiguous alignments: | 192,412 |
| No feature assigned: | 8,730,368 |
| Missing chromosome in annotation: | 266,425 |
| Not aligned: | 5,957,702 |
Reads genomic origin
| Exonic: | 62,097,508 / 87.67% |
| Intronic: | 5,327,260 / 7.52% |
| Intergenic: | 3,403,108 / 4.8% |
| Intronic/intergenic overlapping exon: | 2,426,717 / 3.43% |
Transcript coverage profile
| 5' bias: | 0.27 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.14 |
Junction analysis
| Reads at junctions: | 19,049,154 |
| ACCT | 5.51% |
| AGGT | 4.75% |
| AGGA | 3.62% |
| ATCT | 3.6% |
| TCCT | 3.34% |
| GCCT | 3.13% |
| AGCT | 2.68% |
| AGGC | 2.39% |
| CCCT | 2.38% |
| AGAT | 2.3% |
| TTCT | 2.17% |
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