Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:37:09 GMT 2023 |
| BAM file: | SRX7354114.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): | 66,094,328 / 66,036,400 |
| Number of aligned pairs (without duplicates): | 66,030,416 |
| Total number of alignments: | 140,408,542 |
| Number of secondary alignments: | 8,277,814 |
| Number of non-unique alignments: | 12,731,072 |
| Aligned to genes: | 105,866,826 |
| Ambiguous alignments: | 417,785 |
| No feature assigned: | 20,327,486 |
| Missing chromosome in annotation: | 1,065,373 |
| Not aligned: | 6,184,588 |
Reads genomic origin
| Exonic: | 105,866,826 / 83.89% |
| Intronic: | 13,218,117 / 10.47% |
| Intergenic: | 7,109,369 / 5.63% |
| Intronic/intergenic overlapping exon: | 4,960,922 / 3.93% |
Transcript coverage profile
| 5' bias: | 0.44 |
| 3' bias: | 0.29 |
| 5'-3' bias: | 1.66 |
Junction analysis
| Reads at junctions: | 42,584,929 |
| ACCT | 5.18% |
| AGGT | 4.71% |
| GCCT | 3.7% |
| TCCT | 3.51% |
| ATCT | 3.49% |
| AGGA | 3.38% |
| AGCT | 2.81% |
| CCCT | 2.77% |
| AGGC | 2.51% |
| TTCT | 2.21% |
| AGAT | 2.13% |
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