Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:57:49 GMT 2023 |
| BAM file: | SRX7354261.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): | 46,467,889 / 46,415,739 |
| Number of aligned pairs (without duplicates): | 46,391,186 |
| Total number of alignments: | 99,528,063 |
| Number of secondary alignments: | 6,644,435 |
| Number of non-unique alignments: | 10,313,707 |
| Aligned to genes: | 78,071,355 |
| Ambiguous alignments: | 385,191 |
| No feature assigned: | 9,970,882 |
| Missing chromosome in annotation: | 786,928 |
| Not aligned: | 2,447,362 |
Reads genomic origin
| Exonic: | 78,071,355 / 88.67% |
| Intronic: | 6,463,156 / 7.34% |
| Intergenic: | 3,507,726 / 3.98% |
| Intronic/intergenic overlapping exon: | 4,719,965 / 5.36% |
Transcript coverage profile
| 5' bias: | 0.25 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.95 |
Junction analysis
| Reads at junctions: | 28,142,784 |
| ACCT | 5.52% |
| TCCT | 5.13% |
| ATCT | 4.53% |
| AGGT | 4.16% |
| CCCT | 3.29% |
| GCCT | 3.18% |
| AGGA | 2.91% |
| TTCT | 2.36% |
| AGGC | 2.22% |
| GTCT | 2.13% |
| AGCT | 2.08% |
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