Input data and parameters
Input
Analysis date: | Tue Oct 31 10:02:25 GMT 2023 |
BAM file: | SRX7354379.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): | 45,605,018 / 45,578,202 |
Number of aligned pairs (without duplicates): | 45,557,191 |
Total number of alignments: | 98,959,164 |
Number of secondary alignments: | 7,775,944 |
Number of non-unique alignments: | 12,968,935 |
Aligned to genes: | 75,062,036 |
Ambiguous alignments: | 307,213 |
No feature assigned: | 10,022,293 |
Missing chromosome in annotation: | 598,687 |
Not aligned: | 2,084,512 |
Reads genomic origin
Exonic: | 75,062,036 / 88.22% |
Intronic: | 6,511,748 / 7.65% |
Intergenic: | 3,510,545 / 4.13% |
Intronic/intergenic overlapping exon: | 3,710,751 / 4.36% |
Transcript coverage profile
5' bias: | 0.42 |
3' bias: | 0.23 |
5'-3' bias: | 1.89 |
Junction analysis
Reads at junctions: | 27,115,102 |
ACCT | 5.34% |
AGGT | 4.51% |
TCCT | 3.95% |
ATCT | 3.88% |
GCCT | 3.53% |
AGGA | 3.19% |
CCCT | 2.92% |
AGCT | 2.56% |
AGGC | 2.38% |
TTCT | 2.12% |
AGAT | 1.84% |