Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:39:14 GMT 2023 |
| BAM file: | SRX7354359.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): | 44,654,380 / 44,433,459 |
| Number of aligned pairs (without duplicates): | 44,410,937 |
| Total number of alignments: | 96,690,976 |
| Number of secondary alignments: | 7,603,137 |
| Number of non-unique alignments: | 12,722,812 |
| Aligned to genes: | 74,831,669 |
| Ambiguous alignments: | 325,029 |
| No feature assigned: | 8,303,413 |
| Missing chromosome in annotation: | 508,053 |
| Not aligned: | 7,746,249 |
Reads genomic origin
| Exonic: | 74,831,669 / 90.01% |
| Intronic: | 4,667,738 / 5.61% |
| Intergenic: | 3,635,675 / 4.37% |
| Intronic/intergenic overlapping exon: | 3,380,284 / 4.07% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.97 |
Junction analysis
| Reads at junctions: | 24,445,889 |
| ACCT | 5.09% |
| AGGT | 4.54% |
| ATCT | 4.09% |
| TCCT | 4.06% |
| AGGA | 3.33% |
| GCCT | 3.29% |
| CCCT | 2.93% |
| AGCT | 2.55% |
| AGGC | 2.27% |
| TTCT | 2.07% |
| AGAA | 1.81% |
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