Input data and parameters
Input
Analysis date: | Tue Oct 31 11:45:53 GMT 2023 |
BAM file: | SRX7354406.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): | 35,646,823 / 35,628,472 |
Number of aligned pairs (without duplicates): | 35,625,729 |
Total number of alignments: | 76,108,967 |
Number of secondary alignments: | 4,833,672 |
Number of non-unique alignments: | 8,082,847 |
Aligned to genes: | 60,179,478 |
Ambiguous alignments: | 201,343 |
No feature assigned: | 7,285,622 |
Missing chromosome in annotation: | 359,677 |
Not aligned: | 3,358,803 |
Reads genomic origin
Exonic: | 60,179,478 / 89.2% |
Intronic: | 4,591,958 / 6.81% |
Intergenic: | 2,693,664 / 3.99% |
Intronic/intergenic overlapping exon: | 2,019,412 / 2.99% |
Transcript coverage profile
5' bias: | 0.36 |
3' bias: | 0.18 |
5'-3' bias: | 2.19 |
Junction analysis
Reads at junctions: | 19,150,496 |
ACCT | 5.45% |
AGGT | 4.69% |
AGGA | 3.57% |
ATCT | 3.55% |
TCCT | 3.45% |
GCCT | 3.24% |
AGCT | 2.7% |
CCCT | 2.39% |
AGAT | 2.36% |
AGGC | 2.35% |
TTCT | 2.16% |