Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:49:46 GMT 2023 |
| BAM file: | SRX7354107.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): | 48,135,034 / 48,096,378 |
| Number of aligned pairs (without duplicates): | 48,089,477 |
| Total number of alignments: | 102,371,307 |
| Number of secondary alignments: | 6,139,895 |
| Number of non-unique alignments: | 10,105,013 |
| Aligned to genes: | 81,728,412 |
| Ambiguous alignments: | 258,134 |
| No feature assigned: | 9,824,937 |
| Missing chromosome in annotation: | 454,811 |
| Not aligned: | 7,546,390 |
Reads genomic origin
| Exonic: | 81,728,412 / 89.27% |
| Intronic: | 6,242,147 / 6.82% |
| Intergenic: | 3,582,790 / 3.91% |
| Intronic/intergenic overlapping exon: | 3,182,545 / 3.48% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.99 |
Junction analysis
| Reads at junctions: | 25,396,010 |
| ACCT | 5.16% |
| AGGT | 4.89% |
| ATCT | 3.78% |
| AGGA | 3.55% |
| TCCT | 3.47% |
| GCCT | 2.91% |
| AGCT | 2.75% |
| AGGC | 2.51% |
| CCCT | 2.38% |
| AGAT | 2.12% |
| TTCT | 2.06% |
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