Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:31:59 GMT 2023 |
| BAM file: | SRX7354103.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): | 37,170,068 / 37,146,201 |
| Number of aligned pairs (without duplicates): | 37,143,179 |
| Total number of alignments: | 79,857,218 |
| Number of secondary alignments: | 5,540,949 |
| Number of non-unique alignments: | 9,187,419 |
| Aligned to genes: | 60,000,519 |
| Ambiguous alignments: | 203,725 |
| No feature assigned: | 10,046,243 |
| Missing chromosome in annotation: | 419,312 |
| Not aligned: | 2,332,131 |
Reads genomic origin
| Exonic: | 60,000,519 / 85.66% |
| Intronic: | 7,126,699 / 10.17% |
| Intergenic: | 2,919,544 / 4.17% |
| Intronic/intergenic overlapping exon: | 2,252,447 / 3.22% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.3 |
Junction analysis
| Reads at junctions: | 17,992,106 |
| ACCT | 5.27% |
| AGGT | 4.7% |
| ATCT | 3.76% |
| AGGA | 3.59% |
| TCCT | 3.52% |
| GCCT | 3.03% |
| AGCT | 2.64% |
| CCCT | 2.5% |
| AGGC | 2.37% |
| AGAT | 2.3% |
| TTCT | 2.24% |
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