Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:30:31 GMT 2023 |
| BAM file: | SRX7354050.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): | 77,380,415 / 77,301,187 |
| Number of aligned pairs (without duplicates): | 77,296,257 |
| Total number of alignments: | 164,415,769 |
| Number of secondary alignments: | 9,734,167 |
| Number of non-unique alignments: | 16,163,047 |
| Aligned to genes: | 132,389,326 |
| Ambiguous alignments: | 413,044 |
| No feature assigned: | 14,638,973 |
| Missing chromosome in annotation: | 811,379 |
| Not aligned: | 9,619,044 |
Reads genomic origin
| Exonic: | 132,389,326 / 90.04% |
| Intronic: | 8,397,168 / 5.71% |
| Intergenic: | 6,241,805 / 4.25% |
| Intronic/intergenic overlapping exon: | 5,189,232 / 3.53% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.02 |
Junction analysis
| Reads at junctions: | 47,613,401 |
| ACCT | 5.39% |
| AGGT | 4.71% |
| AGGA | 3.66% |
| ATCT | 3.48% |
| TCCT | 3.35% |
| GCCT | 3.16% |
| AGCT | 2.73% |
| AGGC | 2.43% |
| AGAT | 2.35% |
| CCCT | 2.3% |
| TTCT | 2.11% |
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