Input data and parameters
Input
| Analysis date: | Tue Oct 31 08:56:48 GMT 2023 |
| BAM file: | SRX7354294.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): | 34,593,274 / 34,576,478 |
| Number of aligned pairs (without duplicates): | 34,573,819 |
| Total number of alignments: | 73,369,404 |
| Number of secondary alignments: | 4,199,652 |
| Number of non-unique alignments: | 6,892,288 |
| Aligned to genes: | 57,625,501 |
| Ambiguous alignments: | 223,138 |
| No feature assigned: | 8,323,379 |
| Missing chromosome in annotation: | 305,098 |
| Not aligned: | 1,433,794 |
Reads genomic origin
| Exonic: | 57,625,501 / 87.38% |
| Intronic: | 6,115,455 / 9.27% |
| Intergenic: | 2,207,924 / 3.35% |
| Intronic/intergenic overlapping exon: | 2,190,900 / 3.32% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 19,560,796 |
| ACCT | 5.49% |
| AGGT | 4.65% |
| ATCT | 3.57% |
| AGGA | 3.56% |
| TCCT | 3.35% |
| GCCT | 3.34% |
| AGCT | 2.74% |
| CCCT | 2.41% |
| AGGC | 2.4% |
| AGAT | 2.28% |
| TTCT | 2.17% |

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