Input data and parameters 

Input

Analysis date: Tue Oct 31 01:34:25 GMT 2023
BAM file: SRX7354377.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): 30,554,420 / 30,538,403
Number of aligned pairs (without duplicates): 30,535,503
Total number of alignments: 64,933,637
Number of secondary alignments: 3,840,814
Number of non-unique alignments: 6,333,335
Aligned to genes: 50,371,200
Ambiguous alignments: 183,892
No feature assigned: 7,778,469
Missing chromosome in annotation: 266,741
Not aligned: 1,655,197

Reads genomic origin

Exonic: 50,371,200 / 86.62%
Intronic: 5,613,385 / 9.65%
Intergenic: 2,165,084 / 3.72%
Intronic/intergenic overlapping exon: 1,936,644 / 3.33%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.19
5'-3' bias: 2.01

Junction analysis

Reads at junctions: 16,041,365
ACCT 5.33%
AGGT 4.68%
ATCT 3.58%
AGGA 3.56%
TCCT 3.4%
GCCT 3.24%
AGCT 2.75%
CCCT 2.41%
AGGC 2.37%
AGAT 2.29%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis