Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:41:32 GMT 2023 |
| BAM file: | SRX7354058.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): | 30,722,676 / 30,707,289 |
| Number of aligned pairs (without duplicates): | 30,704,237 |
| Total number of alignments: | 65,730,560 |
| Number of secondary alignments: | 4,300,595 |
| Number of non-unique alignments: | 7,056,188 |
| Aligned to genes: | 50,268,696 |
| Ambiguous alignments: | 184,759 |
| No feature assigned: | 7,883,428 |
| Missing chromosome in annotation: | 337,489 |
| Not aligned: | 2,711,309 |
Reads genomic origin
| Exonic: | 50,268,696 / 86.44% |
| Intronic: | 5,910,722 / 10.16% |
| Intergenic: | 1,972,706 / 3.39% |
| Intronic/intergenic overlapping exon: | 1,884,440 / 3.24% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 16,152,495 |
| ACCT | 5.26% |
| AGGT | 4.69% |
| ATCT | 3.56% |
| AGGA | 3.5% |
| TCCT | 3.49% |
| GCCT | 3.03% |
| AGCT | 2.7% |
| TTCT | 2.52% |
| CCCT | 2.35% |
| AGGC | 2.34% |
| AGAT | 2.31% |
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