Input data and parameters 

Input

Analysis date: Tue Oct 31 10:04:54 GMT 2023
BAM file: SRX7354358.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): 42,797,565 / 42,711,422
Number of aligned pairs (without duplicates): 42,699,579
Total number of alignments: 93,329,116
Number of secondary alignments: 7,820,129
Number of non-unique alignments: 12,071,635
Aligned to genes: 72,395,820
Ambiguous alignments: 303,699
No feature assigned: 7,702,557
Missing chromosome in annotation: 855,405
Not aligned: 7,670,411

Reads genomic origin

Exonic: 72,395,820 / 90.38%
Intronic: 5,017,387 / 6.26%
Intergenic: 2,685,170 / 3.35%
Intronic/intergenic overlapping exon: 3,132,959 / 3.91%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.2
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 23,233,004
ACCT 5.4%
AGGT 4.49%
TCCT 4.18%
ATCT 4.03%
AGGA 3.15%
GCCT 3.05%
CCCT 2.67%
TTCT 2.43%
AGCT 2.23%
AGGC 2.21%
AGAT 1.79%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis