Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:47:20 GMT 2023 |
| BAM file: | SRX7354129.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): | 37,846,508 / 37,803,185 |
| Number of aligned pairs (without duplicates): | 37,797,570 |
| Total number of alignments: | 81,001,076 |
| Number of secondary alignments: | 5,351,383 |
| Number of non-unique alignments: | 8,965,612 |
| Aligned to genes: | 61,492,000 |
| Ambiguous alignments: | 187,081 |
| No feature assigned: | 9,965,995 |
| Missing chromosome in annotation: | 390,388 |
| Not aligned: | 5,564,533 |
Reads genomic origin
| Exonic: | 61,492,000 / 86.05% |
| Intronic: | 7,076,652 / 9.9% |
| Intergenic: | 2,889,343 / 4.04% |
| Intronic/intergenic overlapping exon: | 3,149,678 / 4.41% |
Transcript coverage profile
| 5' bias: | 0.44 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 21,948,690 |
| ACCT | 5.07% |
| AGGT | 4.74% |
| ATCT | 3.84% |
| TCCT | 3.7% |
| AGGA | 3.53% |
| AGCT | 2.86% |
| GCCT | 2.78% |
| AGGC | 2.44% |
| CCCT | 2.24% |
| TTCT | 2.21% |
| AGAT | 2.17% |
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