Input data and parameters
Input
Analysis date: | Tue Oct 31 09:59:00 GMT 2023 |
BAM file: | SRX7354387.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): | 30,788,458 / 30,763,449 |
Number of aligned pairs (without duplicates): | 30,758,537 |
Total number of alignments: | 66,871,404 |
Number of secondary alignments: | 5,319,497 |
Number of non-unique alignments: | 7,533,256 |
Aligned to genes: | 50,622,681 |
Ambiguous alignments: | 178,517 |
No feature assigned: | 7,573,315 |
Missing chromosome in annotation: | 963,635 |
Not aligned: | 3,529,367 |
Reads genomic origin
Exonic: | 50,622,681 / 86.99% |
Intronic: | 4,878,184 / 8.38% |
Intergenic: | 2,695,131 / 4.63% |
Intronic/intergenic overlapping exon: | 2,057,971 / 3.54% |
Transcript coverage profile
5' bias: | 0.35 |
3' bias: | 0.24 |
5'-3' bias: | 1.8 |
Junction analysis
Reads at junctions: | 16,259,498 |
ACCT | 5.22% |
AGGT | 4.6% |
ATCT | 3.73% |
TCCT | 3.39% |
AGGA | 3.35% |
TTCT | 3.33% |
GCCT | 2.99% |
AGCT | 2.68% |
CCCT | 2.43% |
AGGC | 2.27% |
AGAT | 2.15% |