Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:43:06 GMT 2023 |
| BAM file: | SRX7354300.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): | 35,014,892 / 34,979,736 |
| Number of aligned pairs (without duplicates): | 34,975,247 |
| Total number of alignments: | 74,856,037 |
| Number of secondary alignments: | 4,861,409 |
| Number of non-unique alignments: | 7,640,721 |
| Aligned to genes: | 56,256,465 |
| Ambiguous alignments: | 236,793 |
| No feature assigned: | 10,122,166 |
| Missing chromosome in annotation: | 599,892 |
| Not aligned: | 9,356,718 |
Reads genomic origin
| Exonic: | 56,256,465 / 84.75% |
| Intronic: | 6,067,673 / 9.14% |
| Intergenic: | 4,054,493 / 6.11% |
| Intronic/intergenic overlapping exon: | 2,305,369 / 3.47% |
Transcript coverage profile
| 5' bias: | 0.59 |
| 3' bias: | 0.28 |
| 5'-3' bias: | 1.69 |
Junction analysis
| Reads at junctions: | 22,725,376 |
| ACCT | 5.26% |
| AGGT | 4.8% |
| AGGA | 3.51% |
| TCCT | 3.45% |
| ATCT | 3.35% |
| GCCT | 3.33% |
| AGCT | 2.81% |
| CCCT | 2.74% |
| AGGC | 2.48% |
| AGAT | 2.23% |
| TTCT | 2.1% |
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