Input data and parameters
Input
| Analysis date: | Mon Oct 30 12:50:30 GMT 2023 |
| BAM file: | SRX7354204.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): | 47,007,698 / 46,965,345 |
| Number of aligned pairs (without duplicates): | 46,958,020 |
| Total number of alignments: | 99,501,785 |
| Number of secondary alignments: | 5,528,742 |
| Number of non-unique alignments: | 9,254,356 |
| Aligned to genes: | 77,630,490 |
| Ambiguous alignments: | 281,942 |
| No feature assigned: | 12,002,980 |
| Missing chromosome in annotation: | 332,017 |
| Not aligned: | 11,403,601 |
Reads genomic origin
| Exonic: | 77,630,490 / 86.61% |
| Intronic: | 7,854,947 / 8.76% |
| Intergenic: | 4,148,033 / 4.63% |
| Intronic/intergenic overlapping exon: | 3,244,181 / 3.62% |
Transcript coverage profile
| 5' bias: | 0.35 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.01 |
Junction analysis
| Reads at junctions: | 25,195,707 |
| ACCT | 5.25% |
| AGGT | 4.94% |
| AGGA | 3.8% |
| TCCT | 3.52% |
| ATCT | 3.45% |
| GCCT | 2.84% |
| AGCT | 2.72% |
| CCCT | 2.45% |
| AGGC | 2.43% |
| AGAT | 2.42% |
| TTCT | 2.15% |
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