Input data and parameters 

Input

Analysis date: Tue Oct 31 09:10:34 GMT 2023
BAM file: SRX7354287.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): 41,179,078 / 41,163,683
Number of aligned pairs (without duplicates): 41,160,538
Total number of alignments: 88,066,736
Number of secondary alignments: 5,723,975
Number of non-unique alignments: 9,066,266
Aligned to genes: 65,609,315
Ambiguous alignments: 244,345
No feature assigned: 12,500,091
Missing chromosome in annotation: 646,719
Not aligned: 2,350,697

Reads genomic origin

Exonic: 65,609,315 / 84%
Intronic: 7,006,116 / 8.97%
Intergenic: 5,493,975 / 7.03%
Intronic/intergenic overlapping exon: 2,781,279 / 3.56%

Transcript coverage profile

5' bias: 0.51
3' bias: 0.26
5'-3' bias: 1.93

Junction analysis

Reads at junctions: 23,410,277
ACCT 5.15%
AGGT 4.77%
ATCT 3.54%
AGGA 3.53%
TCCT 3.49%
GCCT 3.27%
AGCT 2.78%
CCCT 2.71%
AGGC 2.44%
AGAT 2.19%
TTCT 2.18%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis