Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:47:01 GMT 2023 |
| BAM file: | SRX7354080.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): | 34,002,932 / 33,975,508 |
| Number of aligned pairs (without duplicates): | 33,968,964 |
| Total number of alignments: | 72,131,249 |
| Number of secondary alignments: | 4,152,809 |
| Number of non-unique alignments: | 6,944,748 |
| Aligned to genes: | 57,037,667 |
| Ambiguous alignments: | 177,139 |
| No feature assigned: | 7,714,469 |
| Missing chromosome in annotation: | 257,226 |
| Not aligned: | 6,031,544 |
Reads genomic origin
| Exonic: | 57,037,667 / 88.09% |
| Intronic: | 5,294,726 / 8.18% |
| Intergenic: | 2,419,743 / 3.74% |
| Intronic/intergenic overlapping exon: | 2,261,035 / 3.49% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.79 |
Junction analysis
| Reads at junctions: | 18,601,844 |
| ACCT | 5.34% |
| AGGT | 4.87% |
| ATCT | 3.82% |
| TCCT | 3.59% |
| AGGA | 3.57% |
| GCCT | 3.07% |
| AGCT | 2.89% |
| AGGC | 2.4% |
| CCCT | 2.23% |
| AGAT | 2.11% |
| TTCT | 1.97% |
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