Input data and parameters 

Input

Analysis date: Tue Oct 31 15:55:56 GMT 2023
BAM file: SRX7354392.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): 44,727,881 / 44,703,078
Number of aligned pairs (without duplicates): 44,696,610
Total number of alignments: 95,141,445
Number of secondary alignments: 5,710,486
Number of non-unique alignments: 9,154,232
Aligned to genes: 73,332,745
Ambiguous alignments: 284,453
No feature assigned: 11,882,841
Missing chromosome in annotation: 487,174
Not aligned: 2,412,497

Reads genomic origin

Exonic: 73,332,745 / 86.06%
Intronic: 9,145,377 / 10.73%
Intergenic: 2,737,464 / 3.21%
Intronic/intergenic overlapping exon: 3,176,893 / 3.73%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.21
5'-3' bias: 1.71

Junction analysis

Reads at junctions: 25,989,169
ACCT 5.17%
AGGT 4.69%
AGGA 3.56%
ATCT 3.5%
TCCT 3.38%
GCCT 2.99%
AGCT 2.82%
AGGC 2.33%
AGAT 2.32%
CCCT 2.31%
TTCT 2.26%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis