Input data and parameters
Input
Analysis date: | Sun Oct 29 12:33:38 GMT 2023 |
BAM file: | SRX7354145.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): | 42,978,960 / 42,957,840 |
Number of aligned pairs (without duplicates): | 42,950,386 |
Total number of alignments: | 92,496,504 |
Number of secondary alignments: | 6,559,704 |
Number of non-unique alignments: | 9,876,622 |
Aligned to genes: | 74,257,857 |
Ambiguous alignments: | 284,308 |
No feature assigned: | 7,137,539 |
Missing chromosome in annotation: | 940,178 |
Not aligned: | 2,070,928 |
Reads genomic origin
Exonic: | 74,257,857 / 91.23% |
Intronic: | 4,317,226 / 5.3% |
Intergenic: | 2,820,313 / 3.46% |
Intronic/intergenic overlapping exon: | 2,811,043 / 3.45% |
Transcript coverage profile
5' bias: | 0.23 |
3' bias: | 0.19 |
5'-3' bias: | 2.09 |
Junction analysis
Reads at junctions: | 21,278,777 |
ACCT | 5.1% |
AGGT | 4.93% |
TCCT | 4.02% |
ATCT | 3.88% |
AGGA | 3.51% |
CCCT | 2.84% |
GCCT | 2.69% |
AGCT | 2.43% |
AGGC | 2.34% |
TTCT | 2.18% |
AGAA | 2.05% |