Input data and parameters 

Input

Analysis date: Mon Oct 30 11:23:58 GMT 2023
BAM file: SRX7354166.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): 47,119,735 / 47,092,084
Number of aligned pairs (without duplicates): 47,083,896
Total number of alignments: 101,381,944
Number of secondary alignments: 7,170,125
Number of non-unique alignments: 10,608,722
Aligned to genes: 78,941,921
Ambiguous alignments: 322,740
No feature assigned: 10,482,553
Missing chromosome in annotation: 1,026,008
Not aligned: 2,996,215

Reads genomic origin

Exonic: 78,941,921 / 88.28%
Intronic: 7,992,235 / 8.94%
Intergenic: 2,490,318 / 2.78%
Intronic/intergenic overlapping exon: 3,449,233 / 3.86%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.18
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 26,927,555
ACCT 5.23%
AGGT 4.7%
TCCT 3.75%
ATCT 3.63%
AGGA 3.44%
GCCT 2.92%
AGCT 2.55%
CCCT 2.54%
AGGC 2.34%
TTCT 2.32%
AGAT 2.06%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis