Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:07:05 GMT 2023 |
| BAM file: | SRX7354265.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): | 50,331,865 / 50,302,897 |
| Number of aligned pairs (without duplicates): | 50,295,572 |
| Total number of alignments: | 113,335,126 |
| Number of secondary alignments: | 12,700,364 |
| Number of non-unique alignments: | 15,445,862 |
| Aligned to genes: | 81,489,453 |
| Ambiguous alignments: | 233,628 |
| No feature assigned: | 12,478,984 |
| Missing chromosome in annotation: | 3,687,199 |
| Not aligned: | 2,699,334 |
Reads genomic origin
| Exonic: | 81,489,453 / 86.72% |
| Intronic: | 7,991,507 / 8.5% |
| Intergenic: | 4,487,477 / 4.78% |
| Intronic/intergenic overlapping exon: | 4,026,144 / 4.28% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 2.16 |
Junction analysis
| Reads at junctions: | 22,937,847 |
| ACCT | 5.03% |
| AGGT | 4.58% |
| AGGA | 3.62% |
| ATCT | 3.61% |
| TCCT | 3.35% |
| GCCT | 3% |
| AGCT | 2.83% |
| TTCT | 2.38% |
| CCCT | 2.37% |
| AGAT | 2.3% |
| AGGC | 2.29% |

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