Input data and parameters
Input
| Analysis date: | Tue Oct 31 14:11:25 GMT 2023 |
| BAM file: | SRX7354400.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): | 41,742,648 / 41,709,172 |
| Number of aligned pairs (without duplicates): | 41,684,098 |
| Total number of alignments: | 89,817,040 |
| Number of secondary alignments: | 6,365,220 |
| Number of non-unique alignments: | 10,447,660 |
| Aligned to genes: | 70,943,514 |
| Ambiguous alignments: | 291,173 |
| No feature assigned: | 7,613,445 |
| Missing chromosome in annotation: | 521,248 |
| Not aligned: | 1,352,324 |
Reads genomic origin
| Exonic: | 70,943,514 / 90.31% |
| Intronic: | 4,472,544 / 5.69% |
| Intergenic: | 3,140,901 / 4% |
| Intronic/intergenic overlapping exon: | 3,352,922 / 4.27% |
Transcript coverage profile
| 5' bias: | 0.29 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 2.03 |
Junction analysis
| Reads at junctions: | 24,405,704 |
| ACCT | 5.45% |
| TCCT | 4.47% |
| AGGT | 4.33% |
| ATCT | 4.22% |
| GCCT | 3.52% |
| AGGA | 2.86% |
| CCCT | 2.86% |
| AGCT | 2.41% |
| AGGC | 2.32% |
| TTCT | 2.18% |
| TCCC | 2.14% |
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