Input data and parameters
Input
| Analysis date: | Sun Oct 29 11:39:44 GMT 2023 |
| BAM file: | SRX7354098.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): | 40,954,169 / 40,907,589 |
| Number of aligned pairs (without duplicates): | 40,903,546 |
| Total number of alignments: | 87,732,681 |
| Number of secondary alignments: | 5,870,923 |
| Number of non-unique alignments: | 10,179,784 |
| Aligned to genes: | 67,926,279 |
| Ambiguous alignments: | 225,748 |
| No feature assigned: | 9,080,845 |
| Missing chromosome in annotation: | 320,025 |
| Not aligned: | 6,518,952 |
Reads genomic origin
| Exonic: | 67,926,279 / 88.21% |
| Intronic: | 5,496,337 / 7.14% |
| Intergenic: | 3,584,508 / 4.65% |
| Intronic/intergenic overlapping exon: | 2,721,326 / 3.53% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.97 |
Junction analysis
| Reads at junctions: | 20,121,487 |
| ACCT | 5.34% |
| AGGT | 4.62% |
| ATCT | 3.64% |
| AGGA | 3.49% |
| TCCT | 3.42% |
| GCCT | 3.35% |
| AGCT | 2.68% |
| AGGC | 2.42% |
| CCCT | 2.39% |
| AGAT | 2.2% |
| TTCT | 2.16% |
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