Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:52:45 GMT 2023 |
| BAM file: | SRX7354312.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): | 55,368,107 / 55,155,603 |
| Number of aligned pairs (without duplicates): | 55,120,104 |
| Total number of alignments: | 124,092,572 |
| Number of secondary alignments: | 13,568,862 |
| Number of non-unique alignments: | 17,328,367 |
| Aligned to genes: | 77,991,680 |
| Ambiguous alignments: | 315,486 |
| No feature assigned: | 25,175,853 |
| Missing chromosome in annotation: | 3,281,186 |
| Not aligned: | 14,242,764 |
Reads genomic origin
| Exonic: | 77,991,680 / 75.6% |
| Intronic: | 13,694,504 / 13.27% |
| Intergenic: | 11,481,349 / 11.13% |
| Intronic/intergenic overlapping exon: | 4,859,254 / 4.71% |
Transcript coverage profile
| 5' bias: | 0.27 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.67 |
Junction analysis
| Reads at junctions: | 30,403,066 |
| ACCT | 5.07% |
| AGGT | 4.54% |
| TCCT | 3.92% |
| ATCT | 3.63% |
| AGGA | 3.16% |
| GCCT | 3.07% |
| CCCT | 2.65% |
| AGCT | 2.35% |
| TTCT | 2.27% |
| AGGC | 2.26% |
| AGGG | 2.12% |
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