Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:20:05 GMT 2023 |
| BAM file: | SRX7354132.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): | 40,190,538 / 40,167,626 |
| Number of aligned pairs (without duplicates): | 40,164,887 |
| Total number of alignments: | 85,428,938 |
| Number of secondary alignments: | 5,070,774 |
| Number of non-unique alignments: | 8,256,367 |
| Aligned to genes: | 67,024,224 |
| Ambiguous alignments: | 232,030 |
| No feature assigned: | 9,463,493 |
| Missing chromosome in annotation: | 452,824 |
| Not aligned: | 2,767,706 |
Reads genomic origin
| Exonic: | 67,024,224 / 87.63% |
| Intronic: | 6,455,871 / 8.44% |
| Intergenic: | 3,007,622 / 3.93% |
| Intronic/intergenic overlapping exon: | 2,779,965 / 3.63% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.92 |
Junction analysis
| Reads at junctions: | 21,867,686 |
| ACCT | 5.42% |
| AGGT | 4.66% |
| ATCT | 3.63% |
| AGGA | 3.56% |
| TCCT | 3.49% |
| GCCT | 3.16% |
| AGCT | 2.78% |
| CCCT | 2.49% |
| AGGC | 2.4% |
| AGAT | 2.26% |
| TTCT | 2.07% |
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