Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:20:12 GMT 2023 |
| BAM file: | SRX7354258.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): | 113,813,918 / 113,735,862 |
| Number of aligned pairs (without duplicates): | 113,711,237 |
| Total number of alignments: | 248,352,025 |
| Number of secondary alignments: | 20,802,245 |
| Number of non-unique alignments: | 31,490,268 |
| Aligned to genes: | 192,093,773 |
| Ambiguous alignments: | 753,767 |
| No feature assigned: | 21,296,539 |
| Missing chromosome in annotation: | 2,717,678 |
| Not aligned: | 11,235,276 |
Reads genomic origin
| Exonic: | 192,093,773 / 90.02% |
| Intronic: | 12,791,682 / 5.99% |
| Intergenic: | 8,504,857 / 3.99% |
| Intronic/intergenic overlapping exon: | 9,332,208 / 4.37% |
Transcript coverage profile
| 5' bias: | 0.18 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.06 |
Junction analysis
| Reads at junctions: | 67,932,498 |
| ACCT | 5.22% |
| TCCT | 4.56% |
| ATCT | 4.38% |
| AGGT | 4.35% |
| AGGA | 3.07% |
| CCCT | 2.98% |
| GCCT | 2.36% |
| AGGC | 2.27% |
| AGCT | 2.07% |
| TTCT | 1.94% |
| AGAA | 1.72% |
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