Input data and parameters 

Input

Analysis date: Mon Oct 30 09:31:59 GMT 2023
BAM file: SRX7354103.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): 37,170,068 / 37,146,201
Number of aligned pairs (without duplicates): 37,143,179
Total number of alignments: 79,857,218
Number of secondary alignments: 5,540,949
Number of non-unique alignments: 9,187,419
Aligned to genes: 60,000,519
Ambiguous alignments: 203,725
No feature assigned: 10,046,243
Missing chromosome in annotation: 419,312
Not aligned: 2,332,131

Reads genomic origin

Exonic: 60,000,519 / 85.66%
Intronic: 7,126,699 / 10.17%
Intergenic: 2,919,544 / 4.17%
Intronic/intergenic overlapping exon: 2,252,447 / 3.22%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.18
5'-3' bias: 2.3

Junction analysis

Reads at junctions: 17,992,106
ACCT 5.27%
AGGT 4.7%
ATCT 3.76%
AGGA 3.59%
TCCT 3.52%
GCCT 3.03%
AGCT 2.64%
CCCT 2.5%
AGGC 2.37%
AGAT 2.3%
TTCT 2.24%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis