Input data and parameters
Input
Analysis date: | Tue Oct 31 01:25:20 GMT 2023 |
BAM file: | SRX7354308.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): | 35,229,330 / 35,184,606 |
Number of aligned pairs (without duplicates): | 35,181,118 |
Total number of alignments: | 75,243,595 |
Number of secondary alignments: | 4,829,659 |
Number of non-unique alignments: | 8,154,856 |
Aligned to genes: | 58,393,474 |
Ambiguous alignments: | 204,378 |
No feature assigned: | 8,169,029 |
Missing chromosome in annotation: | 321,858 |
Not aligned: | 4,455,770 |
Reads genomic origin
Exonic: | 58,393,474 / 87.73% |
Intronic: | 5,111,403 / 7.68% |
Intergenic: | 3,057,626 / 4.59% |
Intronic/intergenic overlapping exon: | 2,177,958 / 3.27% |
Transcript coverage profile
5' bias: | 0.33 |
3' bias: | 0.19 |
5'-3' bias: | 2.1 |
Junction analysis
Reads at junctions: | 16,811,769 |
ACCT | 5.17% |
AGGT | 4.8% |
ATCT | 3.81% |
AGGA | 3.57% |
TCCT | 3.37% |
GCCT | 3.16% |
AGCT | 2.77% |
CCCT | 2.54% |
AGGC | 2.44% |
AGAT | 2.33% |
TTCT | 2.1% |