Input data and parameters 

Input

Analysis date: Mon Oct 30 20:02:50 GMT 2023
BAM file: SRX7354211.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): 37,325,262 / 37,301,759
Number of aligned pairs (without duplicates): 37,298,503
Total number of alignments: 79,710,118
Number of secondary alignments: 5,083,097
Number of non-unique alignments: 8,268,978
Aligned to genes: 62,159,195
Ambiguous alignments: 184,407
No feature assigned: 8,635,007
Missing chromosome in annotation: 462,531
Not aligned: 3,748,421

Reads genomic origin

Exonic: 62,159,195 / 87.8%
Intronic: 5,454,367 / 7.7%
Intergenic: 3,180,640 / 4.49%
Intronic/intergenic overlapping exon: 2,287,536 / 3.23%

Transcript coverage profile

5' bias: 0.4
3' bias: 0.16
5'-3' bias: 2.18

Junction analysis

Reads at junctions: 17,997,211
ACCT 5.36%
AGGT 4.95%
AGGA 3.75%
ATCT 3.49%
TCCT 3.35%
GCCT 3.1%
AGCT 2.75%
AGGC 2.46%
CCCT 2.37%
AGAT 2.31%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis