Input data and parameters 

Input

Analysis date: Mon Oct 30 23:19:45 GMT 2023
BAM file: SRX7354280.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): 71,928,397 / 71,870,885
Number of aligned pairs (without duplicates): 71,866,315
Total number of alignments: 152,381,753
Number of secondary alignments: 8,582,471
Number of non-unique alignments: 13,456,609
Aligned to genes: 121,875,632
Ambiguous alignments: 428,573
No feature assigned: 15,633,925
Missing chromosome in annotation: 987,014
Not aligned: 2,996,254

Reads genomic origin

Exonic: 121,875,632 / 88.63%
Intronic: 10,067,722 / 7.32%
Intergenic: 5,566,203 / 4.05%
Intronic/intergenic overlapping exon: 4,981,885 / 3.62%

Transcript coverage profile

5' bias: 0.48
3' bias: 0.15
5'-3' bias: 2.22

Junction analysis

Reads at junctions: 50,756,574
ACCT 5.38%
AGGT 4.79%
AGGA 3.61%
ATCT 3.55%
GCCT 3.21%
TCCT 3.18%
AGCT 2.76%
AGGC 2.46%
CCCT 2.45%
TTCT 2.29%
AGAT 2.27%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis