Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:24:49 GMT 2023 |
| BAM file: | SRX7354349.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): | 45,068,723 / 44,952,878 |
| Number of aligned pairs (without duplicates): | 44,934,915 |
| Total number of alignments: | 96,660,658 |
| Number of secondary alignments: | 6,639,057 |
| Number of non-unique alignments: | 10,940,999 |
| Aligned to genes: | 72,602,270 |
| Ambiguous alignments: | 284,043 |
| No feature assigned: | 12,589,307 |
| Missing chromosome in annotation: | 244,039 |
| Not aligned: | 7,240,043 |
Reads genomic origin
| Exonic: | 72,602,270 / 85.22% |
| Intronic: | 10,527,468 / 12.36% |
| Intergenic: | 2,061,839 / 2.42% |
| Intronic/intergenic overlapping exon: | 3,610,128 / 4.24% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.83 |
Junction analysis
| Reads at junctions: | 28,092,943 |
| ACCT | 5.8% |
| AGGT | 4.78% |
| TCCT | 3.76% |
| AGGA | 3.76% |
| ATCT | 3.45% |
| AGCT | 2.68% |
| AGAT | 2.42% |
| TTCT | 2.28% |
| GCCT | 2.26% |
| AGGC | 2.24% |
| CCCT | 2.22% |
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