Input data and parameters 

Input

Analysis date: Sun Oct 29 12:20:05 GMT 2023
BAM file: SRX7354132.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): 40,190,538 / 40,167,626
Number of aligned pairs (without duplicates): 40,164,887
Total number of alignments: 85,428,938
Number of secondary alignments: 5,070,774
Number of non-unique alignments: 8,256,367
Aligned to genes: 67,024,224
Ambiguous alignments: 232,030
No feature assigned: 9,463,493
Missing chromosome in annotation: 452,824
Not aligned: 2,767,706

Reads genomic origin

Exonic: 67,024,224 / 87.63%
Intronic: 6,455,871 / 8.44%
Intergenic: 3,007,622 / 3.93%
Intronic/intergenic overlapping exon: 2,779,965 / 3.63%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.2
5'-3' bias: 1.92

Junction analysis

Reads at junctions: 21,867,686
ACCT 5.42%
AGGT 4.66%
ATCT 3.63%
AGGA 3.56%
TCCT 3.49%
GCCT 3.16%
AGCT 2.78%
CCCT 2.49%
AGGC 2.4%
AGAT 2.26%
TTCT 2.07%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis