Input data and parameters 

Input

Analysis date: Tue Oct 31 09:19:14 GMT 2023
BAM file: SRX7354307.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): 47,187,521 / 47,142,426
Number of aligned pairs (without duplicates): 47,137,633
Total number of alignments: 101,333,103
Number of secondary alignments: 7,003,156
Number of non-unique alignments: 10,355,728
Aligned to genes: 79,004,146
Ambiguous alignments: 276,424
No feature assigned: 10,498,987
Missing chromosome in annotation: 1,197,818
Not aligned: 9,256,473

Reads genomic origin

Exonic: 79,004,146 / 88.27%
Intronic: 5,265,352 / 5.88%
Intergenic: 5,233,635 / 5.85%
Intronic/intergenic overlapping exon: 3,086,654 / 3.45%

Transcript coverage profile

5' bias: 0.56
3' bias: 0.28
5'-3' bias: 1.81

Junction analysis

Reads at junctions: 28,092,846
ACCT 5.11%
AGGT 4.73%
ATCT 3.53%
AGGA 3.48%
TCCT 3.45%
GCCT 3.31%
AGCT 2.86%
CCCT 2.69%
AGGC 2.41%
TTCT 2.22%
AGAT 2.14%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis