Input data and parameters
Input
Analysis date: | Tue Oct 31 09:32:30 GMT 2023 |
BAM file: | SRX7354306.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): | 74,436,389 / 74,382,890 |
Number of aligned pairs (without duplicates): | 74,373,190 |
Total number of alignments: | 159,970,734 |
Number of secondary alignments: | 11,151,455 |
Number of non-unique alignments: | 16,050,091 |
Aligned to genes: | 130,152,536 |
Ambiguous alignments: | 592,704 |
No feature assigned: | 11,231,764 |
Missing chromosome in annotation: | 1,943,639 |
Not aligned: | 4,123,807 |
Reads genomic origin
Exonic: | 130,152,536 / 92.06% |
Intronic: | 6,605,421 / 4.67% |
Intergenic: | 4,626,343 / 3.27% |
Intronic/intergenic overlapping exon: | 5,498,545 / 3.89% |
Transcript coverage profile
5' bias: | 0.16 |
3' bias: | 0.15 |
5'-3' bias: | 1.98 |
Junction analysis
Reads at junctions: | 49,983,960 |
ACCT | 5.27% |
TCCT | 4.68% |
AGGT | 4.32% |
ATCT | 4.18% |
CCCT | 3.2% |
AGGA | 2.85% |
AGGC | 2.45% |
GCCT | 2.42% |
AGCT | 2.14% |
TTCT | 1.9% |
GTCT | 1.84% |