Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:42:58 GMT 2023 |
| BAM file: | SRX7354137.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): | 34,113,264 / 34,095,273 |
| Number of aligned pairs (without duplicates): | 34,093,215 |
| Total number of alignments: | 73,017,422 |
| Number of secondary alignments: | 4,808,885 |
| Number of non-unique alignments: | 7,812,601 |
| Aligned to genes: | 58,194,985 |
| Ambiguous alignments: | 198,509 |
| No feature assigned: | 6,358,416 |
| Missing chromosome in annotation: | 452,911 |
| Not aligned: | 2,073,297 |
Reads genomic origin
| Exonic: | 58,194,985 / 90.15% |
| Intronic: | 4,028,008 / 6.24% |
| Intergenic: | 2,330,408 / 3.61% |
| Intronic/intergenic overlapping exon: | 2,068,573 / 3.2% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.82 |
Junction analysis
| Reads at junctions: | 19,251,592 |
| ACCT | 5.33% |
| AGGT | 4.72% |
| ATCT | 3.59% |
| AGGA | 3.54% |
| TCCT | 3.39% |
| GCCT | 3.23% |
| AGCT | 2.81% |
| CCCT | 2.52% |
| AGGC | 2.37% |
| AGAT | 2.25% |
| TTCT | 2.16% |
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