Input data and parameters 

Input

Analysis date: Sun Oct 29 01:37:42 GMT 2023
BAM file: SRX7354060.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): 34,098,842 / 34,079,141
Number of aligned pairs (without duplicates): 34,075,658
Total number of alignments: 72,510,309
Number of secondary alignments: 4,332,326
Number of non-unique alignments: 6,931,902
Aligned to genes: 54,809,512
Ambiguous alignments: 188,763
No feature assigned: 10,190,684
Missing chromosome in annotation: 389,448
Not aligned: 2,861,333

Reads genomic origin

Exonic: 54,809,512 / 84.32%
Intronic: 7,253,630 / 11.16%
Intergenic: 2,937,054 / 4.52%
Intronic/intergenic overlapping exon: 2,187,237 / 3.36%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.22
5'-3' bias: 1.93

Junction analysis

Reads at junctions: 17,134,932
ACCT 5.35%
AGGT 4.74%
AGGA 3.57%
ATCT 3.54%
TCCT 3.45%
GCCT 3.12%
AGCT 2.76%
CCCT 2.38%
AGGC 2.37%
AGAT 2.32%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis