Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:40:01 GMT 2023 |
| BAM file: | SRX7354171.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): | 27,293,282 / 27,267,676 |
| Number of aligned pairs (without duplicates): | 27,263,053 |
| Total number of alignments: | 58,166,001 |
| Number of secondary alignments: | 3,605,043 |
| Number of non-unique alignments: | 5,893,126 |
| Aligned to genes: | 46,193,349 |
| Ambiguous alignments: | 170,118 |
| No feature assigned: | 5,617,542 |
| Missing chromosome in annotation: | 291,866 |
| Not aligned: | 5,049,338 |
Reads genomic origin
| Exonic: | 46,193,349 / 89.16% |
| Intronic: | 2,905,566 / 5.61% |
| Intergenic: | 2,711,976 / 5.23% |
| Intronic/intergenic overlapping exon: | 1,943,327 / 3.75% |
Transcript coverage profile
| 5' bias: | 0.23 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.74 |
Junction analysis
| Reads at junctions: | 15,887,057 |
| ACCT | 6.04% |
| ATCT | 4.38% |
| TCCT | 4.32% |
| AGGT | 4.23% |
| GCCT | 3.79% |
| AGGA | 2.87% |
| CCCT | 2.77% |
| TTCT | 2.32% |
| TCCC | 2.31% |
| AGCT | 2.16% |
| AGGC | 2.13% |
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