Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:21:40 GMT 2023 |
| BAM file: | SRX7354292.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): | 32,513,660 / 32,502,871 |
| Number of aligned pairs (without duplicates): | 32,500,359 |
| Total number of alignments: | 68,830,076 |
| Number of secondary alignments: | 3,813,545 |
| Number of non-unique alignments: | 5,982,218 |
| Aligned to genes: | 54,881,193 |
| Ambiguous alignments: | 190,290 |
| No feature assigned: | 7,350,482 |
| Missing chromosome in annotation: | 425,893 |
| Not aligned: | 911,743 |
Reads genomic origin
| Exonic: | 54,881,193 / 88.19% |
| Intronic: | 5,056,174 / 8.12% |
| Intergenic: | 2,294,308 / 3.69% |
| Intronic/intergenic overlapping exon: | 2,151,538 / 3.46% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 2.23 |
Junction analysis
| Reads at junctions: | 18,961,980 |
| ACCT | 5.61% |
| AGGT | 4.69% |
| ATCT | 3.65% |
| AGGA | 3.56% |
| TCCT | 3.41% |
| GCCT | 3.13% |
| AGCT | 2.72% |
| AGGC | 2.42% |
| AGAT | 2.29% |
| CCCT | 2.25% |
| TTCT | 2.09% |
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