Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:20:50 GMT 2023 |
| BAM file: | SRX7354295.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): | 49,861,222 / 49,840,990 |
| Number of aligned pairs (without duplicates): | 49,836,748 |
| Total number of alignments: | 107,394,066 |
| Number of secondary alignments: | 7,691,854 |
| Number of non-unique alignments: | 12,470,032 |
| Aligned to genes: | 76,243,711 |
| Ambiguous alignments: | 235,128 |
| No feature assigned: | 17,668,982 |
| Missing chromosome in annotation: | 776,213 |
| Not aligned: | 2,796,648 |
Reads genomic origin
| Exonic: | 76,243,711 / 81.19% |
| Intronic: | 8,596,107 / 9.15% |
| Intergenic: | 9,072,875 / 9.66% |
| Intronic/intergenic overlapping exon: | 3,213,557 / 3.42% |
Transcript coverage profile
| 5' bias: | 0.57 |
| 3' bias: | 0.28 |
| 5'-3' bias: | 1.84 |
Junction analysis
| Reads at junctions: | 24,698,259 |
| ACCT | 5.02% |
| AGGT | 4.64% |
| TCCT | 3.58% |
| ATCT | 3.47% |
| AGGA | 3.44% |
| GCCT | 3.34% |
| AGCT | 2.82% |
| CCCT | 2.69% |
| AGGC | 2.36% |
| TTCT | 2.24% |
| AGAT | 2.12% |
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