Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:36:56 GMT 2023 |
| BAM file: | SRX7354284.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): | 30,942,860 / 30,912,396 |
| Number of aligned pairs (without duplicates): | 30,903,913 |
| Total number of alignments: | 65,593,417 |
| Number of secondary alignments: | 3,738,161 |
| Number of non-unique alignments: | 6,107,027 |
| Aligned to genes: | 53,030,121 |
| Ambiguous alignments: | 177,837 |
| No feature assigned: | 5,976,943 |
| Missing chromosome in annotation: | 301,489 |
| Not aligned: | 6,618,840 |
Reads genomic origin
| Exonic: | 53,030,121 / 89.87% |
| Intronic: | 3,390,613 / 5.75% |
| Intergenic: | 2,586,330 / 4.38% |
| Intronic/intergenic overlapping exon: | 2,033,187 / 3.45% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 2.28 |
Junction analysis
| Reads at junctions: | 16,695,825 |
| ACCT | 5.94% |
| AGGT | 4.48% |
| ATCT | 3.9% |
| TCCT | 3.88% |
| GCCT | 3.43% |
| AGGA | 3.24% |
| CCCT | 2.5% |
| AGCT | 2.37% |
| AGGC | 2.33% |
| TTCT | 2.11% |
| AGAT | 1.95% |
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