Input data and parameters
Input
Analysis date: | Tue Oct 31 09:56:55 GMT 2023 |
BAM file: | SRX7354325.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): | 59,848,435 / 59,804,695 |
Number of aligned pairs (without duplicates): | 59,794,158 |
Total number of alignments: | 129,845,037 |
Number of secondary alignments: | 10,191,907 |
Number of non-unique alignments: | 15,790,042 |
Aligned to genes: | 100,950,740 |
Ambiguous alignments: | 414,973 |
No feature assigned: | 11,588,553 |
Missing chromosome in annotation: | 1,100,729 |
Not aligned: | 7,798,324 |
Reads genomic origin
Exonic: | 100,950,740 / 89.7% |
Intronic: | 6,257,046 / 5.56% |
Intergenic: | 5,331,507 / 4.74% |
Intronic/intergenic overlapping exon: | 4,848,282 / 4.31% |
Transcript coverage profile
5' bias: | 0.05 |
3' bias: | 0.07 |
5'-3' bias: | 2.8 |
Junction analysis
Reads at junctions: | 32,715,761 |
TCCT | 5.61% |
ACCT | 4.9% |
AGGT | 4.37% |
ATCT | 4.18% |
CCCT | 3.93% |
AGGA | 3.29% |
AGGC | 2.08% |
TGCT | 1.98% |
AGAC | 1.93% |
AGCT | 1.83% |
GTCT | 1.83% |