Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:48:50 GMT 2023 |
| BAM file: | SRX7354332.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): | 45,707,210 / 45,654,997 |
| Number of aligned pairs (without duplicates): | 45,649,318 |
| Total number of alignments: | 97,476,975 |
| Number of secondary alignments: | 6,114,768 |
| Number of non-unique alignments: | 10,229,321 |
| Aligned to genes: | 76,545,582 |
| Ambiguous alignments: | 264,051 |
| No feature assigned: | 10,006,434 |
| Missing chromosome in annotation: | 431,587 |
| Not aligned: | 8,856,645 |
Reads genomic origin
| Exonic: | 76,545,582 / 88.44% |
| Intronic: | 6,409,296 / 7.41% |
| Intergenic: | 3,597,138 / 4.16% |
| Intronic/intergenic overlapping exon: | 3,035,717 / 3.51% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.99 |
Junction analysis
| Reads at junctions: | 23,513,927 |
| ACCT | 5.34% |
| AGGT | 4.72% |
| ATCT | 3.9% |
| AGGA | 3.6% |
| TCCT | 3.51% |
| GCCT | 3.23% |
| CCCT | 2.68% |
| AGCT | 2.63% |
| AGGC | 2.41% |
| AGAT | 2.26% |
| TTCT | 2.23% |
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