Input data and parameters
Input
Analysis date: | Mon Oct 30 22:32:26 GMT 2023 |
BAM file: | SRX7354264.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): | 30,295,332 / 30,277,361 |
Number of aligned pairs (without duplicates): | 30,273,897 |
Total number of alignments: | 64,293,821 |
Number of secondary alignments: | 3,721,128 |
Number of non-unique alignments: | 5,676,950 |
Aligned to genes: | 48,761,861 |
Ambiguous alignments: | 178,229 |
No feature assigned: | 9,174,220 |
Missing chromosome in annotation: | 502,561 |
Not aligned: | 1,267,935 |
Reads genomic origin
Exonic: | 48,761,861 / 84.16% |
Intronic: | 6,293,625 / 10.86% |
Intergenic: | 2,880,595 / 4.97% |
Intronic/intergenic overlapping exon: | 2,238,650 / 3.86% |
Transcript coverage profile
5' bias: | 0.52 |
3' bias: | 0.25 |
5'-3' bias: | 1.96 |
Junction analysis
Reads at junctions: | 18,223,811 |
ACCT | 5.21% |
AGGT | 4.73% |
TCCT | 3.58% |
ATCT | 3.57% |
AGGA | 3.39% |
GCCT | 3.33% |
AGCT | 2.68% |
CCCT | 2.68% |
AGGC | 2.5% |
TTCT | 2.25% |
AGAT | 2.16% |