Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:57:09 GMT 2023 |
| BAM file: | SRX7354283.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): | 42,649,122 / 42,613,151 |
| Number of aligned pairs (without duplicates): | 42,608,922 |
| Total number of alignments: | 90,274,213 |
| Number of secondary alignments: | 5,011,940 |
| Number of non-unique alignments: | 8,354,323 |
| Aligned to genes: | 72,315,358 |
| Ambiguous alignments: | 243,279 |
| No feature assigned: | 8,991,031 |
| Missing chromosome in annotation: | 370,222 |
| Not aligned: | 2,996,667 |
Reads genomic origin
| Exonic: | 72,315,358 / 88.94% |
| Intronic: | 5,750,993 / 7.07% |
| Intergenic: | 3,240,038 / 3.98% |
| Intronic/intergenic overlapping exon: | 2,943,711 / 3.62% |
Transcript coverage profile
| 5' bias: | 0.45 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 2.11 |
Junction analysis
| Reads at junctions: | 25,562,411 |
| ACCT | 5.42% |
| AGGT | 4.85% |
| AGGA | 3.75% |
| ATCT | 3.56% |
| TCCT | 3.43% |
| GCCT | 2.88% |
| AGCT | 2.71% |
| AGGC | 2.42% |
| CCCT | 2.34% |
| AGAT | 2.33% |
| TTCT | 2.25% |
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