Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:28:25 GMT 2023 |
| BAM file: | SRX7354138.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): | 43,715,050 / 43,665,052 |
| Number of aligned pairs (without duplicates): | 43,646,149 |
| Total number of alignments: | 94,560,051 |
| Number of secondary alignments: | 7,179,949 |
| Number of non-unique alignments: | 11,098,380 |
| Aligned to genes: | 71,866,756 |
| Ambiguous alignments: | 327,264 |
| No feature assigned: | 10,319,834 |
| Missing chromosome in annotation: | 947,817 |
| Not aligned: | 2,527,784 |
Reads genomic origin
| Exonic: | 71,866,756 / 87.44% |
| Intronic: | 7,595,518 / 9.24% |
| Intergenic: | 2,724,316 / 3.31% |
| Intronic/intergenic overlapping exon: | 3,765,337 / 4.58% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.84 |
Junction analysis
| Reads at junctions: | 30,056,330 |
| ACCT | 5.3% |
| AGGT | 4.76% |
| TCCT | 3.56% |
| ATCT | 3.56% |
| AGGA | 3.34% |
| GCCT | 3.2% |
| AGCT | 2.78% |
| CCCT | 2.71% |
| AGGC | 2.45% |
| TTCT | 2.06% |
| AGAT | 2.03% |
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