Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:56:47 GMT 2023 |
| BAM file: | SRX7354215.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): | 35,236,109 / 35,216,179 |
| Number of aligned pairs (without duplicates): | 35,211,699 |
| Total number of alignments: | 74,819,370 |
| Number of secondary alignments: | 4,367,082 |
| Number of non-unique alignments: | 7,124,971 |
| Aligned to genes: | 57,450,195 |
| Ambiguous alignments: | 187,156 |
| No feature assigned: | 9,669,543 |
| Missing chromosome in annotation: | 387,505 |
| Not aligned: | 3,278,352 |
Reads genomic origin
| Exonic: | 57,450,195 / 85.59% |
| Intronic: | 6,841,838 / 10.19% |
| Intergenic: | 2,827,705 / 4.21% |
| Intronic/intergenic overlapping exon: | 2,366,734 / 3.53% |
Transcript coverage profile
| 5' bias: | 0.29 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 17,933,348 |
| ACCT | 5.24% |
| AGGT | 4.72% |
| AGGA | 3.75% |
| ATCT | 3.62% |
| TCCT | 3.32% |
| AGCT | 2.8% |
| GCCT | 2.79% |
| AGAT | 2.55% |
| AGGC | 2.37% |
| CCCT | 2.3% |
| TTCT | 2.28% |
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