Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:59:15 GMT 2023 |
| BAM file: | SRX7354319.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): | 49,041,933 / 48,986,119 |
| Number of aligned pairs (without duplicates): | 48,978,285 |
| Total number of alignments: | 104,078,901 |
| Number of secondary alignments: | 6,050,849 |
| Number of non-unique alignments: | 10,244,468 |
| Aligned to genes: | 79,897,812 |
| Ambiguous alignments: | 251,771 |
| No feature assigned: | 13,335,464 |
| Missing chromosome in annotation: | 349,386 |
| Not aligned: | 9,068,550 |
Reads genomic origin
| Exonic: | 79,897,812 / 85.7% |
| Intronic: | 8,661,107 / 9.29% |
| Intergenic: | 4,674,357 / 5.01% |
| Intronic/intergenic overlapping exon: | 3,459,083 / 3.71% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 2.4 |
Junction analysis
| Reads at junctions: | 23,721,100 |
| ACCT | 5.39% |
| AGGT | 4.76% |
| AGGA | 3.75% |
| TCCT | 3.54% |
| ATCT | 3.52% |
| GCCT | 2.91% |
| AGCT | 2.71% |
| AGAT | 2.38% |
| AGGC | 2.33% |
| CCCT | 2.27% |
| TTCT | 2.11% |
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