Input data and parameters
Input
| Analysis date: | Sun Oct 29 11:42:31 GMT 2023 |
| BAM file: | SRX7354094.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): | 49,414,447 / 49,365,990 |
| Number of aligned pairs (without duplicates): | 49,357,278 |
| Total number of alignments: | 105,863,399 |
| Number of secondary alignments: | 7,082,962 |
| Number of non-unique alignments: | 11,549,153 |
| Aligned to genes: | 83,589,758 |
| Ambiguous alignments: | 294,154 |
| No feature assigned: | 9,814,887 |
| Missing chromosome in annotation: | 615,447 |
| Not aligned: | 3,301,757 |
Reads genomic origin
| Exonic: | 83,589,758 / 89.49% |
| Intronic: | 6,367,889 / 6.82% |
| Intergenic: | 3,446,998 / 3.69% |
| Intronic/intergenic overlapping exon: | 3,446,152 / 3.69% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.82 |
Junction analysis
| Reads at junctions: | 27,428,961 |
| ACCT | 5.16% |
| AGGT | 4.61% |
| TCCT | 3.89% |
| ATCT | 3.85% |
| AGGA | 3.36% |
| GCCT | 3.1% |
| CCCT | 2.62% |
| AGCT | 2.61% |
| AGGC | 2.27% |
| TTCT | 2.13% |
| AGAT | 1.97% |
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