Input data and parameters 

Input

Analysis date: Tue Oct 31 10:16:33 GMT 2023
BAM file: SRX7354384.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): 56,137,570 / 56,076,345
Number of aligned pairs (without duplicates): 56,069,686
Total number of alignments: 122,057,020
Number of secondary alignments: 9,843,105
Number of non-unique alignments: 16,731,113
Aligned to genes: 94,862,845
Ambiguous alignments: 299,716
No feature assigned: 9,490,222
Missing chromosome in annotation: 673,124
Not aligned: 5,289,045

Reads genomic origin

Exonic: 94,862,845 / 90.91%
Intronic: 4,011,818 / 3.84%
Intergenic: 5,478,404 / 5.25%
Intronic/intergenic overlapping exon: 3,548,376 / 3.4%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.2
5'-3' bias: 1.92

Junction analysis

Reads at junctions: 26,780,016
ACCT 5.39%
AGGT 4.46%
TCCT 3.85%
ATCT 3.78%
AGGA 3.38%
GCCT 3.2%
CCCT 2.46%
AGCT 2.38%
AGGC 2.26%
TTCT 2.26%
AGAT 1.96%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis