Input data and parameters
Input
Analysis date: | Mon Oct 30 09:47:06 GMT 2023 |
BAM file: | SRX7354187.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): | 48,712,103 / 48,648,376 |
Number of aligned pairs (without duplicates): | 48,626,652 |
Total number of alignments: | 112,351,257 |
Number of secondary alignments: | 14,990,778 |
Number of non-unique alignments: | 17,645,355 |
Aligned to genes: | 79,739,866 |
Ambiguous alignments: | 342,960 |
No feature assigned: | 10,013,261 |
Missing chromosome in annotation: | 4,609,815 |
Not aligned: | 2,921,695 |
Reads genomic origin
Exonic: | 79,739,866 / 88.84% |
Intronic: | 6,707,396 / 7.47% |
Intergenic: | 3,305,865 / 3.68% |
Intronic/intergenic overlapping exon: | 4,575,031 / 5.1% |
Transcript coverage profile
5' bias: | 0.41 |
3' bias: | 0.26 |
5'-3' bias: | 1.81 |
Junction analysis
Reads at junctions: | 30,252,804 |
ACCT | 5.66% |
AGGT | 4.37% |
TCCT | 4.04% |
ATCT | 3.74% |
GCCT | 3.51% |
AGGA | 3.15% |
CCCT | 2.78% |
AGCT | 2.61% |
AGGC | 2.34% |
TTCT | 2.21% |
TCCC | 1.86% |