Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:40:38 GMT 2023 |
| BAM file: | SRX7354270.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): | 43,202,493 / 43,174,046 |
| Number of aligned pairs (without duplicates): | 43,168,864 |
| Total number of alignments: | 92,494,107 |
| Number of secondary alignments: | 6,117,568 |
| Number of non-unique alignments: | 10,020,271 |
| Aligned to genes: | 63,940,017 |
| Ambiguous alignments: | 235,535 |
| No feature assigned: | 17,759,121 |
| Missing chromosome in annotation: | 539,163 |
| Not aligned: | 4,295,981 |
Reads genomic origin
| Exonic: | 63,940,017 / 78.26% |
| Intronic: | 10,038,079 / 12.29% |
| Intergenic: | 7,721,042 / 9.45% |
| Intronic/intergenic overlapping exon: | 2,938,616 / 3.6% |
Transcript coverage profile
| 5' bias: | 0.44 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 2.14 |
Junction analysis
| Reads at junctions: | 25,502,424 |
| ACCT | 5.06% |
| AGGT | 4.81% |
| AGGA | 3.54% |
| ATCT | 3.53% |
| TCCT | 3.5% |
| GCCT | 3.23% |
| AGCT | 2.7% |
| CCCT | 2.62% |
| AGGC | 2.44% |
| TTCT | 2.29% |
| AGAT | 2.19% |
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