Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:23:58 GMT 2023 |
| BAM file: | SRX7354166.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): | 47,119,735 / 47,092,084 |
| Number of aligned pairs (without duplicates): | 47,083,896 |
| Total number of alignments: | 101,381,944 |
| Number of secondary alignments: | 7,170,125 |
| Number of non-unique alignments: | 10,608,722 |
| Aligned to genes: | 78,941,921 |
| Ambiguous alignments: | 322,740 |
| No feature assigned: | 10,482,553 |
| Missing chromosome in annotation: | 1,026,008 |
| Not aligned: | 2,996,215 |
Reads genomic origin
| Exonic: | 78,941,921 / 88.28% |
| Intronic: | 7,992,235 / 8.94% |
| Intergenic: | 2,490,318 / 2.78% |
| Intronic/intergenic overlapping exon: | 3,449,233 / 3.86% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.94 |
Junction analysis
| Reads at junctions: | 26,927,555 |
| ACCT | 5.23% |
| AGGT | 4.7% |
| TCCT | 3.75% |
| ATCT | 3.63% |
| AGGA | 3.44% |
| GCCT | 2.92% |
| AGCT | 2.55% |
| CCCT | 2.54% |
| AGGC | 2.34% |
| TTCT | 2.32% |
| AGAT | 2.06% |
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