Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:25:49 GMT 2023 |
| BAM file: | SRX7354120.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): | 34,162,043 / 34,124,206 |
| Number of aligned pairs (without duplicates): | 34,119,872 |
| Total number of alignments: | 72,676,831 |
| Number of secondary alignments: | 4,390,582 |
| Number of non-unique alignments: | 7,425,841 |
| Aligned to genes: | 56,537,285 |
| Ambiguous alignments: | 180,774 |
| No feature assigned: | 8,249,034 |
| Missing chromosome in annotation: | 283,897 |
| Not aligned: | 6,625,723 |
Reads genomic origin
| Exonic: | 56,537,285 / 87.27% |
| Intronic: | 4,845,094 / 7.48% |
| Intergenic: | 3,403,940 / 5.25% |
| Intronic/intergenic overlapping exon: | 2,333,272 / 3.6% |
Transcript coverage profile
| 5' bias: | 0.43 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 17,009,269 |
| ACCT | 5.28% |
| AGGT | 4.83% |
| AGGA | 3.65% |
| ATCT | 3.56% |
| TCCT | 3.52% |
| GCCT | 2.9% |
| AGCT | 2.76% |
| CCCT | 2.43% |
| AGGC | 2.41% |
| AGAT | 2.32% |
| TTCT | 2.15% |
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