Input data and parameters 

Input

Analysis date: Mon Oct 30 22:35:13 GMT 2023
BAM file: SRX7354253.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): 30,549,913 / 30,537,413
Number of aligned pairs (without duplicates): 30,535,104
Total number of alignments: 65,375,283
Number of secondary alignments: 4,287,957
Number of non-unique alignments: 6,973,828
Aligned to genes: 51,978,879
Ambiguous alignments: 203,655
No feature assigned: 5,863,617
Missing chromosome in annotation: 355,304
Not aligned: 1,130,136

Reads genomic origin

Exonic: 51,978,879 / 89.86%
Intronic: 3,931,028 / 6.8%
Intergenic: 1,932,589 / 3.34%
Intronic/intergenic overlapping exon: 1,689,528 / 2.92%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.22
5'-3' bias: 1.97

Junction analysis

Reads at junctions: 17,452,726
ACCT 5.42%
AGGT 4.65%
ATCT 3.6%
AGGA 3.52%
TCCT 3.48%
GCCT 3.37%
AGCT 2.61%
CCCT 2.41%
AGGC 2.35%
AGAT 2.27%
TTCT 2.18%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis