Input data and parameters 

Input

Analysis date: Sun Oct 29 01:14:09 GMT 2023
BAM file: SRX7354051.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): 30,808,479 / 30,773,980
Number of aligned pairs (without duplicates): 30,770,445
Total number of alignments: 65,570,732
Number of secondary alignments: 3,988,273
Number of non-unique alignments: 6,483,249
Aligned to genes: 49,051,672
Ambiguous alignments: 171,830
No feature assigned: 9,599,912
Missing chromosome in annotation: 264,069
Not aligned: 3,812,783

Reads genomic origin

Exonic: 49,051,672 / 83.63%
Intronic: 6,873,216 / 11.72%
Intergenic: 2,726,696 / 4.65%
Intronic/intergenic overlapping exon: 2,217,322 / 3.78%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.28
5'-3' bias: 1.63

Junction analysis

Reads at junctions: 17,544,371
ACCT 4.92%
AGGT 4.69%
AGGA 3.56%
TCCT 3.54%
ATCT 3.53%
AGCT 3.13%
GCCT 2.87%
CCCT 2.57%
AGGC 2.32%
TTCT 2.12%
AGAT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis