Input data and parameters
Input
Analysis date: | Sun Oct 29 12:26:23 GMT 2023 |
BAM file: | SRX7354074.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): | 91,252,929 / 91,043,857 |
Number of aligned pairs (without duplicates): | 91,027,741 |
Total number of alignments: | 195,027,732 |
Number of secondary alignments: | 12,730,946 |
Number of non-unique alignments: | 20,435,273 |
Aligned to genes: | 145,789,904 |
Ambiguous alignments: | 573,821 |
No feature assigned: | 27,080,025 |
Missing chromosome in annotation: | 1,148,709 |
Not aligned: | 23,316,472 |
Reads genomic origin
Exonic: | 145,789,904 / 84.34% |
Intronic: | 16,343,125 / 9.45% |
Intergenic: | 10,736,900 / 6.21% |
Intronic/intergenic overlapping exon: | 6,816,246 / 3.94% |
Transcript coverage profile
5' bias: | 0.39 |
3' bias: | 0.32 |
5'-3' bias: | 1.62 |
Junction analysis
Reads at junctions: | 57,521,364 |
ACCT | 5.07% |
AGGT | 4.7% |
TCCT | 3.93% |
ATCT | 3.73% |
GCCT | 3.28% |
AGGA | 3.16% |
CCCT | 2.8% |
AGCT | 2.56% |
AGGC | 2.52% |
TTCT | 2.19% |
AGAT | 1.89% |