Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:40:44 GMT 2023 |
| BAM file: | SRX7354102.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): | 30,076,716 / 30,054,357 |
| Number of aligned pairs (without duplicates): | 30,051,643 |
| Total number of alignments: | 65,234,475 |
| Number of secondary alignments: | 5,103,402 |
| Number of non-unique alignments: | 7,138,623 |
| Aligned to genes: | 49,286,293 |
| Ambiguous alignments: | 171,429 |
| No feature assigned: | 7,688,363 |
| Missing chromosome in annotation: | 949,767 |
| Not aligned: | 3,301,137 |
Reads genomic origin
| Exonic: | 49,286,293 / 86.51% |
| Intronic: | 5,449,698 / 9.57% |
| Intergenic: | 2,238,665 / 3.93% |
| Intronic/intergenic overlapping exon: | 1,926,888 / 3.38% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 2.04 |
Junction analysis
| Reads at junctions: | 15,160,237 |
| ACCT | 5.53% |
| AGGT | 4.75% |
| ATCT | 3.68% |
| AGGA | 3.62% |
| TCCT | 3.6% |
| GCCT | 3.17% |
| AGCT | 2.73% |
| CCCT | 2.39% |
| AGGC | 2.35% |
| AGAT | 2.27% |
| TTCT | 2.12% |
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