Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:50:39 GMT 2023 |
| BAM file: | SRX7354378.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): | 31,509,835 / 31,488,128 |
| Number of aligned pairs (without duplicates): | 31,484,352 |
| Total number of alignments: | 66,851,293 |
| Number of secondary alignments: | 3,853,330 |
| Number of non-unique alignments: | 6,258,286 |
| Aligned to genes: | 51,773,257 |
| Ambiguous alignments: | 174,767 |
| No feature assigned: | 8,315,266 |
| Missing chromosome in annotation: | 329,717 |
| Not aligned: | 2,825,283 |
Reads genomic origin
| Exonic: | 51,773,257 / 86.16% |
| Intronic: | 5,801,773 / 9.66% |
| Intergenic: | 2,513,493 / 4.18% |
| Intronic/intergenic overlapping exon: | 2,111,905 / 3.51% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.76 |
Junction analysis
| Reads at junctions: | 16,724,217 |
| ACCT | 5.33% |
| AGGT | 4.72% |
| ATCT | 3.59% |
| AGGA | 3.52% |
| TCCT | 3.27% |
| GCCT | 3.2% |
| AGCT | 2.83% |
| AGGC | 2.43% |
| CCCT | 2.39% |
| AGAT | 2.32% |
| TTCT | 2.17% |
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