Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:01:50 GMT 2023 |
| BAM file: | SRX7354084.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): | 34,617,799 / 34,576,411 |
| Number of aligned pairs (without duplicates): | 34,570,775 |
| Total number of alignments: | 73,699,286 |
| Number of secondary alignments: | 4,505,076 |
| Number of non-unique alignments: | 7,243,392 |
| Aligned to genes: | 56,955,623 |
| Ambiguous alignments: | 175,224 |
| No feature assigned: | 8,864,079 |
| Missing chromosome in annotation: | 460,968 |
| Not aligned: | 6,384,848 |
Reads genomic origin
| Exonic: | 56,955,623 / 86.53% |
| Intronic: | 5,356,399 / 8.14% |
| Intergenic: | 3,507,680 / 5.33% |
| Intronic/intergenic overlapping exon: | 2,413,800 / 3.67% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.27 |
| 5'-3' bias: | 1.61 |
Junction analysis
| Reads at junctions: | 21,066,559 |
| ACCT | 5.01% |
| AGGT | 5% |
| TCCT | 3.73% |
| AGGA | 3.7% |
| ATCT | 3.64% |
| AGCT | 3.08% |
| GCCT | 2.62% |
| AGGC | 2.51% |
| CCCT | 2.33% |
| AGAT | 2.1% |
| TTCT | 1.97% |
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