Input data and parameters 

Input

Analysis date: Sun Oct 29 11:46:16 GMT 2023
BAM file: SRX7354075.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): 46,237,060 / 46,207,369
Number of aligned pairs (without duplicates): 46,199,620
Total number of alignments: 101,510,585
Number of secondary alignments: 9,066,156
Number of non-unique alignments: 12,903,017
Aligned to genes: 79,998,365
Ambiguous alignments: 390,426
No feature assigned: 6,630,267
Missing chromosome in annotation: 1,588,510
Not aligned: 2,564,031

Reads genomic origin

Exonic: 79,998,365 / 92.35%
Intronic: 3,902,471 / 4.5%
Intergenic: 2,727,796 / 3.15%
Intronic/intergenic overlapping exon: 3,592,599 / 4.15%

Transcript coverage profile

5' bias: 0.11
3' bias: 0.12
5'-3' bias: 2.14

Junction analysis

Reads at junctions: 26,631,656
TCCT 5.95%
ACCT 5.33%
ATCT 4.65%
AGGT 4.16%
CCCT 3.67%
AGGA 2.87%
GCCT 2.23%
AGGC 2.21%
GTCT 2.07%
TCCC 1.97%
AGCT 1.93%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis