Input data and parameters
Input
| Analysis date: | Sun Oct 29 13:03:20 GMT 2023 |
| BAM file: | SRX7354185.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): | 45,349,643 / 45,314,964 |
| Number of aligned pairs (without duplicates): | 45,305,278 |
| Total number of alignments: | 97,083,497 |
| Number of secondary alignments: | 6,418,890 |
| Number of non-unique alignments: | 10,426,378 |
| Aligned to genes: | 76,248,076 |
| Ambiguous alignments: | 285,236 |
| No feature assigned: | 9,556,886 |
| Missing chromosome in annotation: | 566,921 |
| Not aligned: | 4,224,585 |
Reads genomic origin
| Exonic: | 76,248,076 / 88.86% |
| Intronic: | 6,508,802 / 7.59% |
| Intergenic: | 3,048,084 / 3.55% |
| Intronic/intergenic overlapping exon: | 3,373,471 / 3.93% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 2.04 |
Junction analysis
| Reads at junctions: | 25,795,808 |
| ACCT | 5.08% |
| AGGT | 4.69% |
| ATCT | 4.19% |
| TCCT | 3.57% |
| GCCT | 3.34% |
| AGGA | 3.32% |
| AGCT | 2.6% |
| CCCT | 2.56% |
| AGGC | 2.34% |
| TTCT | 2.08% |
| AGAT | 1.96% |
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