Input data and parameters 

Input

Analysis date: Tue Oct 31 01:21:40 GMT 2023
BAM file: SRX7354292.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): 32,513,660 / 32,502,871
Number of aligned pairs (without duplicates): 32,500,359
Total number of alignments: 68,830,076
Number of secondary alignments: 3,813,545
Number of non-unique alignments: 5,982,218
Aligned to genes: 54,881,193
Ambiguous alignments: 190,290
No feature assigned: 7,350,482
Missing chromosome in annotation: 425,893
Not aligned: 911,743

Reads genomic origin

Exonic: 54,881,193 / 88.19%
Intronic: 5,056,174 / 8.12%
Intergenic: 2,294,308 / 3.69%
Intronic/intergenic overlapping exon: 2,151,538 / 3.46%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.14
5'-3' bias: 2.23

Junction analysis

Reads at junctions: 18,961,980
ACCT 5.61%
AGGT 4.69%
ATCT 3.65%
AGGA 3.56%
TCCT 3.41%
GCCT 3.13%
AGCT 2.72%
AGGC 2.42%
AGAT 2.29%
CCCT 2.25%
TTCT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis