Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:24:09 GMT 2023 |
| BAM file: | SRX7354233.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): | 35,441,710 / 35,420,204 |
| Number of aligned pairs (without duplicates): | 35,417,097 |
| Total number of alignments: | 74,624,108 |
| Number of secondary alignments: | 3,762,194 |
| Number of non-unique alignments: | 6,244,653 |
| Aligned to genes: | 58,085,125 |
| Ambiguous alignments: | 185,103 |
| No feature assigned: | 9,843,018 |
| Missing chromosome in annotation: | 266,209 |
| Not aligned: | 2,047,928 |
Reads genomic origin
| Exonic: | 58,085,125 / 85.51% |
| Intronic: | 7,152,969 / 10.53% |
| Intergenic: | 2,690,049 / 3.96% |
| Intronic/intergenic overlapping exon: | 2,376,602 / 3.5% |
Transcript coverage profile
| 5' bias: | 0.43 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 2.49 |
Junction analysis
| Reads at junctions: | 18,484,905 |
| ACCT | 5.5% |
| AGGT | 4.73% |
| ATCT | 3.62% |
| AGGA | 3.6% |
| TCCT | 3.54% |
| GCCT | 3.05% |
| AGCT | 2.68% |
| AGGC | 2.39% |
| AGAT | 2.3% |
| CCCT | 2.22% |
| TTCT | 2.11% |
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