Input data and parameters 

Input

Analysis date: Sun Oct 29 01:42:58 GMT 2023
BAM file: SRX7354137.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): 34,113,264 / 34,095,273
Number of aligned pairs (without duplicates): 34,093,215
Total number of alignments: 73,017,422
Number of secondary alignments: 4,808,885
Number of non-unique alignments: 7,812,601
Aligned to genes: 58,194,985
Ambiguous alignments: 198,509
No feature assigned: 6,358,416
Missing chromosome in annotation: 452,911
Not aligned: 2,073,297

Reads genomic origin

Exonic: 58,194,985 / 90.15%
Intronic: 4,028,008 / 6.24%
Intergenic: 2,330,408 / 3.61%
Intronic/intergenic overlapping exon: 2,068,573 / 3.2%

Transcript coverage profile

5' bias: 0.48
3' bias: 0.25
5'-3' bias: 1.82

Junction analysis

Reads at junctions: 19,251,592
ACCT 5.33%
AGGT 4.72%
ATCT 3.59%
AGGA 3.54%
TCCT 3.39%
GCCT 3.23%
AGCT 2.81%
CCCT 2.52%
AGGC 2.37%
AGAT 2.25%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis