Input data and parameters 

Input

Analysis date: Tue Oct 31 10:15:52 GMT 2023
BAM file: SRX7354383.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): 73,755,943 / 73,726,879
Number of aligned pairs (without duplicates): 73,717,107
Total number of alignments: 160,008,443
Number of secondary alignments: 12,525,621
Number of non-unique alignments: 20,488,376
Aligned to genes: 125,465,041
Ambiguous alignments: 525,162
No feature assigned: 12,416,909
Missing chromosome in annotation: 1,112,955
Not aligned: 3,607,772

Reads genomic origin

Exonic: 125,465,041 / 90.99%
Intronic: 5,756,691 / 4.18%
Intergenic: 6,660,218 / 4.83%
Intronic/intergenic overlapping exon: 5,399,234 / 3.92%

Transcript coverage profile

5' bias: 0.14
3' bias: 0.13
5'-3' bias: 2.05

Junction analysis

Reads at junctions: 39,845,894
ACCT 5.21%
TCCT 5.08%
ATCT 4.49%
AGGT 4.37%
CCCT 3.26%
AGGA 3.07%
GCCT 2.65%
AGGC 2.37%
TTCT 2.06%
AGCT 1.94%
TCCC 1.72%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis