Input data and parameters 

Input

Analysis date: Sun Oct 29 12:46:09 GMT 2023
BAM file: SRX7354077.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): 77,080,409 / 76,937,265
Number of aligned pairs (without duplicates): 76,926,539
Total number of alignments: 163,471,885
Number of secondary alignments: 9,454,211
Number of non-unique alignments: 14,747,971
Aligned to genes: 127,773,214
Ambiguous alignments: 464,162
No feature assigned: 19,359,488
Missing chromosome in annotation: 1,127,050
Not aligned: 12,614,118

Reads genomic origin

Exonic: 127,773,214 / 86.84%
Intronic: 12,508,592 / 8.5%
Intergenic: 6,850,896 / 4.66%
Intronic/intergenic overlapping exon: 6,118,082 / 4.16%

Transcript coverage profile

5' bias: 0.49
3' bias: 0.25
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 53,602,932
ACCT 5.15%
AGGT 4.77%
TCCT 3.54%
AGGA 3.44%
ATCT 3.36%
GCCT 3.12%
AGCT 2.81%
CCCT 2.53%
AGGC 2.41%
AGAT 2.18%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis