Input data and parameters 

Input

Analysis date: Tue Oct 31 01:26:43 GMT 2023
BAM file: SRX7354255.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): 45,572,320 / 45,536,597
Number of aligned pairs (without duplicates): 45,527,428
Total number of alignments: 96,927,407
Number of secondary alignments: 5,818,490
Number of non-unique alignments: 9,072,807
Aligned to genes: 76,087,009
Ambiguous alignments: 250,992
No feature assigned: 10,846,445
Missing chromosome in annotation: 670,154
Not aligned: 3,871,977

Reads genomic origin

Exonic: 76,087,009 / 87.52%
Intronic: 7,618,470 / 8.76%
Intergenic: 3,227,975 / 3.71%
Intronic/intergenic overlapping exon: 3,550,082 / 4.08%

Transcript coverage profile

5' bias: 0.29
3' bias: 0.15
5'-3' bias: 1.93

Junction analysis

Reads at junctions: 24,048,279
ACCT 5.57%
AGGT 4.6%
ATCT 3.72%
TCCT 3.58%
AGGA 3.42%
GCCT 3.27%
AGCT 2.5%
CCCT 2.45%
AGGC 2.31%
TTCT 2.07%
AGAT 2.04%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis