Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:42:15 GMT 2023 |
| BAM file: | SRX7354147.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): | 38,166,533 / 38,136,365 |
| Number of aligned pairs (without duplicates): | 38,131,931 |
| Total number of alignments: | 81,076,961 |
| Number of secondary alignments: | 4,774,063 |
| Number of non-unique alignments: | 7,892,544 |
| Aligned to genes: | 60,627,608 |
| Ambiguous alignments: | 260,879 |
| No feature assigned: | 11,921,810 |
| Missing chromosome in annotation: | 374,120 |
| Not aligned: | 5,729,070 |
Reads genomic origin
| Exonic: | 60,627,608 / 83.57% |
| Intronic: | 7,234,347 / 9.97% |
| Intergenic: | 4,687,463 / 6.46% |
| Intronic/intergenic overlapping exon: | 2,826,480 / 3.9% |
Transcript coverage profile
| 5' bias: | 0.45 |
| 3' bias: | 0.31 |
| 5'-3' bias: | 1.73 |
Junction analysis
| Reads at junctions: | 21,016,047 |
| ACCT | 5.14% |
| AGGT | 4.7% |
| TCCT | 3.71% |
| ATCT | 3.5% |
| AGGA | 3.46% |
| GCCT | 3.39% |
| CCCT | 2.73% |
| AGCT | 2.69% |
| AGGC | 2.48% |
| AGAT | 2.14% |
| TTCT | 2.11% |
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