Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:26:43 GMT 2023 |
| BAM file: | SRX7354255.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): | 45,572,320 / 45,536,597 |
| Number of aligned pairs (without duplicates): | 45,527,428 |
| Total number of alignments: | 96,927,407 |
| Number of secondary alignments: | 5,818,490 |
| Number of non-unique alignments: | 9,072,807 |
| Aligned to genes: | 76,087,009 |
| Ambiguous alignments: | 250,992 |
| No feature assigned: | 10,846,445 |
| Missing chromosome in annotation: | 670,154 |
| Not aligned: | 3,871,977 |
Reads genomic origin
| Exonic: | 76,087,009 / 87.52% |
| Intronic: | 7,618,470 / 8.76% |
| Intergenic: | 3,227,975 / 3.71% |
| Intronic/intergenic overlapping exon: | 3,550,082 / 4.08% |
Transcript coverage profile
| 5' bias: | 0.29 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.93 |
Junction analysis
| Reads at junctions: | 24,048,279 |
| ACCT | 5.57% |
| AGGT | 4.6% |
| ATCT | 3.72% |
| TCCT | 3.58% |
| AGGA | 3.42% |
| GCCT | 3.27% |
| AGCT | 2.5% |
| CCCT | 2.45% |
| AGGC | 2.31% |
| TTCT | 2.07% |
| AGAT | 2.04% |
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