Input data and parameters
Input
| Analysis date: | Sun Oct 29 13:13:37 GMT 2023 |
| BAM file: | SRX7354155.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): | 68,887,389 / 68,839,702 |
| Number of aligned pairs (without duplicates): | 68,835,029 |
| Total number of alignments: | 148,517,519 |
| Number of secondary alignments: | 10,790,428 |
| Number of non-unique alignments: | 15,869,265 |
| Aligned to genes: | 108,680,798 |
| Ambiguous alignments: | 413,738 |
| No feature assigned: | 21,782,492 |
| Missing chromosome in annotation: | 1,771,226 |
| Not aligned: | 3,964,535 |
Reads genomic origin
| Exonic: | 108,680,798 / 83.3% |
| Intronic: | 12,698,113 / 9.73% |
| Intergenic: | 9,084,379 / 6.96% |
| Intronic/intergenic overlapping exon: | 5,075,380 / 3.89% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.37 |
| 5'-3' bias: | 1.51 |
Junction analysis
| Reads at junctions: | 41,706,548 |
| ACCT | 5.01% |
| AGGT | 4.68% |
| TCCT | 3.91% |
| ATCT | 3.66% |
| GCCT | 3.29% |
| AGGA | 3.21% |
| AGCT | 2.73% |
| CCCT | 2.71% |
| TTCT | 2.48% |
| AGGC | 2.45% |
| AGAT | 1.97% |
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