Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:53:24 GMT 2023 |
| BAM file: | SRX7354402.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): | 34,159,486 / 34,105,407 |
| Number of aligned pairs (without duplicates): | 34,101,640 |
| Total number of alignments: | 73,367,407 |
| Number of secondary alignments: | 5,102,514 |
| Number of non-unique alignments: | 8,573,792 |
| Aligned to genes: | 57,701,489 |
| Ambiguous alignments: | 198,929 |
| No feature assigned: | 6,559,532 |
| Missing chromosome in annotation: | 333,665 |
| Not aligned: | 4,379,369 |
Reads genomic origin
| Exonic: | 57,701,489 / 89.79% |
| Intronic: | 3,921,545 / 6.1% |
| Intergenic: | 2,637,987 / 4.11% |
| Intronic/intergenic overlapping exon: | 2,060,095 / 3.21% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.9 |
Junction analysis
| Reads at junctions: | 17,746,189 |
| ACCT | 5.31% |
| AGGT | 4.61% |
| ATCT | 3.8% |
| TCCT | 3.48% |
| AGGA | 3.38% |
| GCCT | 3.24% |
| AGCT | 2.61% |
| CCCT | 2.44% |
| TTCT | 2.42% |
| AGGC | 2.37% |
| AGAT | 2.09% |
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