Input data and parameters
Input
Analysis date: | Tue Oct 31 09:32:03 GMT 2023 |
BAM file: | SRX7354314.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): | 44,621,804 / 44,541,931 |
Number of aligned pairs (without duplicates): | 44,519,442 |
Total number of alignments: | 96,286,785 |
Number of secondary alignments: | 7,123,050 |
Number of non-unique alignments: | 11,214,189 |
Aligned to genes: | 76,533,741 |
Ambiguous alignments: | 332,960 |
No feature assigned: | 7,527,045 |
Missing chromosome in annotation: | 678,850 |
Not aligned: | 5,872,927 |
Reads genomic origin
Exonic: | 76,533,741 / 91.05% |
Intronic: | 4,131,599 / 4.92% |
Intergenic: | 3,395,446 / 4.04% |
Intronic/intergenic overlapping exon: | 3,147,267 / 3.74% |
Transcript coverage profile
5' bias: | 0.1 |
3' bias: | 0.14 |
5'-3' bias: | 1.77 |
Junction analysis
Reads at junctions: | 22,147,650 |
TCCT | 5.27% |
ACCT | 5.09% |
ATCT | 4.57% |
AGGT | 4.19% |
CCCT | 3.49% |
AGGA | 2.83% |
GCCT | 2.39% |
AGGC | 2.37% |
TTCT | 2.1% |
AGCT | 2.05% |
AGAC | 1.92% |