Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:02:50 GMT 2023 |
| BAM file: | SRX7354211.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): | 37,325,262 / 37,301,759 |
| Number of aligned pairs (without duplicates): | 37,298,503 |
| Total number of alignments: | 79,710,118 |
| Number of secondary alignments: | 5,083,097 |
| Number of non-unique alignments: | 8,268,978 |
| Aligned to genes: | 62,159,195 |
| Ambiguous alignments: | 184,407 |
| No feature assigned: | 8,635,007 |
| Missing chromosome in annotation: | 462,531 |
| Not aligned: | 3,748,421 |
Reads genomic origin
| Exonic: | 62,159,195 / 87.8% |
| Intronic: | 5,454,367 / 7.7% |
| Intergenic: | 3,180,640 / 4.49% |
| Intronic/intergenic overlapping exon: | 2,287,536 / 3.23% |
Transcript coverage profile
| 5' bias: | 0.4 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.18 |
Junction analysis
| Reads at junctions: | 17,997,211 |
| ACCT | 5.36% |
| AGGT | 4.95% |
| AGGA | 3.75% |
| ATCT | 3.49% |
| TCCT | 3.35% |
| GCCT | 3.1% |
| AGCT | 2.75% |
| AGGC | 2.46% |
| CCCT | 2.37% |
| AGAT | 2.31% |
| TTCT | 2.11% |
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