Input data and parameters 

Input

Analysis date: Mon Oct 30 23:25:18 GMT 2023
BAM file: SRX7354218.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): 42,972,955 / 42,946,710
Number of aligned pairs (without duplicates): 42,942,617
Total number of alignments: 91,467,467
Number of secondary alignments: 5,547,802
Number of non-unique alignments: 9,164,767
Aligned to genes: 71,532,385
Ambiguous alignments: 287,964
No feature assigned: 10,053,922
Missing chromosome in annotation: 428,429
Not aligned: 5,791,955

Reads genomic origin

Exonic: 71,532,385 / 87.68%
Intronic: 6,472,712 / 7.93%
Intergenic: 3,581,210 / 4.39%
Intronic/intergenic overlapping exon: 3,002,672 / 3.68%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.19
5'-3' bias: 1.75

Junction analysis

Reads at junctions: 23,732,209
ACCT 5.33%
AGGT 4.79%
ATCT 3.85%
TCCT 3.48%
AGGA 3.4%
GCCT 3.24%
CCCT 2.72%
AGCT 2.61%
AGGC 2.45%
TTCT 2.22%
AGAT 2.04%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis