Input data and parameters
Input
Analysis date: | Mon Oct 30 09:28:48 GMT 2023 |
BAM file: | SRX7354154.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): | 43,958,974 / 43,931,656 |
Number of aligned pairs (without duplicates): | 43,920,759 |
Total number of alignments: | 95,778,872 |
Number of secondary alignments: | 7,888,242 |
Number of non-unique alignments: | 11,971,165 |
Aligned to genes: | 74,402,360 |
Ambiguous alignments: | 323,932 |
No feature assigned: | 8,028,480 |
Missing chromosome in annotation: | 1,052,935 |
Not aligned: | 2,309,888 |
Reads genomic origin
Exonic: | 74,402,360 / 90.26% |
Intronic: | 4,889,934 / 5.93% |
Intergenic: | 3,138,546 / 3.81% |
Intronic/intergenic overlapping exon: | 3,715,801 / 4.51% |
Transcript coverage profile
5' bias: | 0.14 |
3' bias: | 0.14 |
5'-3' bias: | 2.02 |
Junction analysis
Reads at junctions: | 23,854,712 |
TCCT | 5.58% |
ACCT | 5.09% |
ATCT | 4.87% |
AGGT | 4.21% |
CCCT | 3.35% |
AGGA | 2.96% |
GCCT | 2.57% |
TTCT | 2.4% |
AGGC | 2.14% |
AGCT | 1.99% |
GTCT | 1.97% |