Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:26:31 GMT 2023 |
| BAM file: | SRX7354239.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): | 34,649,226 / 34,625,806 |
| Number of aligned pairs (without duplicates): | 34,622,944 |
| Total number of alignments: | 73,954,372 |
| Number of secondary alignments: | 4,679,340 |
| Number of non-unique alignments: | 7,872,920 |
| Aligned to genes: | 58,862,729 |
| Ambiguous alignments: | 217,610 |
| No feature assigned: | 6,725,420 |
| Missing chromosome in annotation: | 275,693 |
| Not aligned: | 2,842,106 |
Reads genomic origin
| Exonic: | 58,862,729 / 89.75% |
| Intronic: | 4,435,457 / 6.76% |
| Intergenic: | 2,289,963 / 3.49% |
| Intronic/intergenic overlapping exon: | 1,952,698 / 2.98% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.02 |
Junction analysis
| Reads at junctions: | 19,287,984 |
| ACCT | 5.68% |
| AGGT | 4.99% |
| AGGA | 3.72% |
| TCCT | 3.48% |
| ATCT | 3.47% |
| GCCT | 3.06% |
| AGCT | 2.74% |
| CCCT | 2.44% |
| AGGC | 2.41% |
| AGAT | 2.27% |
| TTCT | 2.14% |
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