Input data and parameters 

Input

Analysis date: Tue Oct 31 09:48:50 GMT 2023
BAM file: SRX7354332.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): 45,707,210 / 45,654,997
Number of aligned pairs (without duplicates): 45,649,318
Total number of alignments: 97,476,975
Number of secondary alignments: 6,114,768
Number of non-unique alignments: 10,229,321
Aligned to genes: 76,545,582
Ambiguous alignments: 264,051
No feature assigned: 10,006,434
Missing chromosome in annotation: 431,587
Not aligned: 8,856,645

Reads genomic origin

Exonic: 76,545,582 / 88.44%
Intronic: 6,409,296 / 7.41%
Intergenic: 3,597,138 / 4.16%
Intronic/intergenic overlapping exon: 3,035,717 / 3.51%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.21
5'-3' bias: 1.99

Junction analysis

Reads at junctions: 23,513,927
ACCT 5.34%
AGGT 4.72%
ATCT 3.9%
AGGA 3.6%
TCCT 3.51%
GCCT 3.23%
CCCT 2.68%
AGCT 2.63%
AGGC 2.41%
AGAT 2.26%
TTCT 2.23%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis