Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:44:32 GMT 2023 |
| BAM file: | SRX7354343.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): | 46,486,442 / 46,468,917 |
| Number of aligned pairs (without duplicates): | 46,461,217 |
| Total number of alignments: | 118,332,330 |
| Number of secondary alignments: | 25,376,971 |
| Number of non-unique alignments: | 23,237,134 |
| Aligned to genes: | 74,638,325 |
| Ambiguous alignments: | 312,368 |
| No feature assigned: | 9,357,783 |
| Missing chromosome in annotation: | 10,786,720 |
| Not aligned: | 2,593,917 |
Reads genomic origin
| Exonic: | 74,638,325 / 88.86% |
| Intronic: | 6,075,923 / 7.23% |
| Intergenic: | 3,281,860 / 3.91% |
| Intronic/intergenic overlapping exon: | 3,113,143 / 3.71% |
Transcript coverage profile
| 5' bias: | 0.2 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.71 |
Junction analysis
| Reads at junctions: | 23,088,997 |
| ACCT | 5.23% |
| AGGT | 4.48% |
| ATCT | 4.29% |
| TCCT | 4.26% |
| CCCT | 3.25% |
| GCCT | 3.18% |
| AGGA | 3.05% |
| AGGC | 2.32% |
| AGCT | 2.17% |
| TTCT | 2.17% |
| GTCT | 1.76% |
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