Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:42:54 GMT 2023 |
| BAM file: | SRX7354112.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): | 37,369,237 / 37,337,032 |
| Number of aligned pairs (without duplicates): | 37,331,193 |
| Total number of alignments: | 79,003,454 |
| Number of secondary alignments: | 4,297,185 |
| Number of non-unique alignments: | 7,179,887 |
| Aligned to genes: | 61,284,155 |
| Ambiguous alignments: | 195,309 |
| No feature assigned: | 10,062,646 |
| Missing chromosome in annotation: | 281,457 |
| Not aligned: | 7,406,477 |
Reads genomic origin
| Exonic: | 61,284,155 / 85.9% |
| Intronic: | 6,906,568 / 9.68% |
| Intergenic: | 3,156,078 / 4.42% |
| Intronic/intergenic overlapping exon: | 2,669,920 / 3.74% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.86 |
Junction analysis
| Reads at junctions: | 19,800,143 |
| ACCT | 5.4% |
| AGGT | 4.68% |
| ATCT | 3.62% |
| AGGA | 3.58% |
| TCCT | 3.41% |
| GCCT | 3.23% |
| AGCT | 2.75% |
| AGGC | 2.41% |
| CCCT | 2.34% |
| AGAT | 2.31% |
| TTCT | 2.11% |
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