Input data and parameters
Input
Analysis date: | Mon Oct 30 20:29:47 GMT 2023 |
BAM file: | SRX7354175.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): | 41,245,765 / 41,226,929 |
Number of aligned pairs (without duplicates): | 41,189,898 |
Total number of alignments: | 88,665,895 |
Number of secondary alignments: | 6,193,201 |
Number of non-unique alignments: | 10,000,213 |
Aligned to genes: | 70,358,603 |
Ambiguous alignments: | 280,250 |
No feature assigned: | 7,468,405 |
Missing chromosome in annotation: | 558,424 |
Not aligned: | 1,322,076 |
Reads genomic origin
Exonic: | 70,358,603 / 90.4% |
Intronic: | 4,320,180 / 5.55% |
Intergenic: | 3,148,225 / 4.05% |
Intronic/intergenic overlapping exon: | 3,529,453 / 4.53% |
Transcript coverage profile
5' bias: | 0.21 |
3' bias: | 0.16 |
5'-3' bias: | 2.72 |
Junction analysis
Reads at junctions: | 23,143,007 |
ACCT | 5.33% |
TCCT | 5.18% |
ATCT | 4.7% |
AGGT | 4.17% |
CCCT | 3.2% |
GCCT | 3.14% |
AGGA | 2.77% |
TTCT | 2.37% |
AGGC | 2.22% |
TCCC | 2.16% |
AGCT | 2.15% |