Input data and parameters
Input
Analysis date: | Mon Oct 30 23:07:05 GMT 2023 |
BAM file: | SRX7354265.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): | 50,331,865 / 50,302,897 |
Number of aligned pairs (without duplicates): | 50,295,572 |
Total number of alignments: | 113,335,126 |
Number of secondary alignments: | 12,700,364 |
Number of non-unique alignments: | 15,445,862 |
Aligned to genes: | 81,489,453 |
Ambiguous alignments: | 233,628 |
No feature assigned: | 12,478,984 |
Missing chromosome in annotation: | 3,687,199 |
Not aligned: | 2,699,334 |
Reads genomic origin
Exonic: | 81,489,453 / 86.72% |
Intronic: | 7,991,507 / 8.5% |
Intergenic: | 4,487,477 / 4.78% |
Intronic/intergenic overlapping exon: | 4,026,144 / 4.28% |
Transcript coverage profile
5' bias: | 0.42 |
3' bias: | 0.13 |
5'-3' bias: | 2.16 |
Junction analysis
Reads at junctions: | 22,937,847 |
ACCT | 5.03% |
AGGT | 4.58% |
AGGA | 3.62% |
ATCT | 3.61% |
TCCT | 3.35% |
GCCT | 3% |
AGCT | 2.83% |
TTCT | 2.38% |
CCCT | 2.37% |
AGAT | 2.3% |
AGGC | 2.29% |