Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:26:01 GMT 2023 |
| BAM file: | SRX7354093.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): | 34,363,830 / 34,335,618 |
| Number of aligned pairs (without duplicates): | 34,332,658 |
| Total number of alignments: | 72,581,466 |
| Number of secondary alignments: | 3,882,018 |
| Number of non-unique alignments: | 6,591,576 |
| Aligned to genes: | 57,633,537 |
| Ambiguous alignments: | 165,409 |
| No feature assigned: | 7,930,936 |
| Missing chromosome in annotation: | 260,008 |
| Not aligned: | 5,652,016 |
Reads genomic origin
| Exonic: | 57,633,537 / 87.9% |
| Intronic: | 4,864,754 / 7.42% |
| Intergenic: | 3,066,182 / 4.68% |
| Intronic/intergenic overlapping exon: | 2,335,073 / 3.56% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.23 |
Junction analysis
| Reads at junctions: | 15,853,368 |
| ACCT | 5.34% |
| AGGT | 4.93% |
| AGGA | 3.68% |
| ATCT | 3.65% |
| TCCT | 3.43% |
| GCCT | 2.9% |
| AGCT | 2.72% |
| CCCT | 2.38% |
| AGGC | 2.36% |
| AGAT | 2.31% |
| TTCT | 2.11% |
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