Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:26:24 GMT 2023 |
| BAM file: | SRX7354068.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): | 33,952,192 / 33,925,553 |
| Number of aligned pairs (without duplicates): | 33,899,710 |
| Total number of alignments: | 74,218,029 |
| Number of secondary alignments: | 6,340,284 |
| Number of non-unique alignments: | 9,194,316 |
| Aligned to genes: | 56,055,718 |
| Ambiguous alignments: | 234,839 |
| No feature assigned: | 7,697,664 |
| Missing chromosome in annotation: | 1,035,492 |
| Not aligned: | 2,449,813 |
Reads genomic origin
| Exonic: | 56,055,718 / 87.93% |
| Intronic: | 5,411,006 / 8.49% |
| Intergenic: | 2,286,658 / 3.59% |
| Intronic/intergenic overlapping exon: | 3,396,109 / 5.33% |
Transcript coverage profile
| 5' bias: | 0.24 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.99 |
Junction analysis
| Reads at junctions: | 20,882,564 |
| ACCT | 5.28% |
| TCCT | 4.48% |
| AGGT | 4.44% |
| ATCT | 4.24% |
| AGGA | 3.08% |
| GCCT | 3% |
| CCCT | 2.96% |
| AGGC | 2.39% |
| AGCT | 2.27% |
| TTCT | 2.05% |
| AGAA | 1.74% |
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