Input data and parameters
Input
Analysis date: | Mon Oct 30 09:23:48 GMT 2023 |
BAM file: | SRX7354156.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): | 31,285,813 / 31,266,266 |
Number of aligned pairs (without duplicates): | 31,263,886 |
Total number of alignments: | 66,202,406 |
Number of secondary alignments: | 3,650,327 |
Number of non-unique alignments: | 6,012,280 |
Aligned to genes: | 51,603,353 |
Ambiguous alignments: | 171,049 |
No feature assigned: | 8,137,511 |
Missing chromosome in annotation: | 278,213 |
Not aligned: | 1,318,855 |
Reads genomic origin
Exonic: | 51,603,353 / 86.38% |
Intronic: | 5,672,063 / 9.49% |
Intergenic: | 2,465,448 / 4.13% |
Intronic/intergenic overlapping exon: | 1,982,629 / 3.32% |
Transcript coverage profile
5' bias: | 0.41 |
3' bias: | 0.16 |
5'-3' bias: | 2.24 |
Junction analysis
Reads at junctions: | 16,710,064 |
ACCT | 5.37% |
AGGT | 4.69% |
AGGA | 3.63% |
ATCT | 3.63% |
TCCT | 3.37% |
GCCT | 3.1% |
AGCT | 2.74% |
AGGC | 2.42% |
AGAT | 2.4% |
CCCT | 2.38% |
TTCT | 2.26% |