Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:07:18 GMT 2023 |
| BAM file: | SRX7354091.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): | 67,086,173 / 67,016,098 |
| Number of aligned pairs (without duplicates): | 67,010,929 |
| Total number of alignments: | 143,113,385 |
| Number of secondary alignments: | 9,011,114 |
| Number of non-unique alignments: | 13,894,813 |
| Aligned to genes: | 104,235,314 |
| Ambiguous alignments: | 413,812 |
| No feature assigned: | 23,480,715 |
| Missing chromosome in annotation: | 1,088,731 |
| Not aligned: | 5,485,655 |
Reads genomic origin
| Exonic: | 104,235,314 / 81.61% |
| Intronic: | 15,407,111 / 12.06% |
| Intergenic: | 8,073,604 / 6.32% |
| Intronic/intergenic overlapping exon: | 5,235,592 / 4.1% |
Transcript coverage profile
| 5' bias: | 0.43 |
| 3' bias: | 0.28 |
| 5'-3' bias: | 1.65 |
Junction analysis
| Reads at junctions: | 44,332,076 |
| ACCT | 5.26% |
| AGGT | 4.62% |
| GCCT | 3.71% |
| TCCT | 3.58% |
| ATCT | 3.43% |
| AGGA | 3.41% |
| CCCT | 2.84% |
| AGCT | 2.81% |
| AGGC | 2.48% |
| AGAT | 2.21% |
| TTCT | 2.12% |
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