Input data and parameters
Input
Analysis date: | Tue Oct 31 01:34:25 GMT 2023 |
BAM file: | SRX7354377.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): | 30,554,420 / 30,538,403 |
Number of aligned pairs (without duplicates): | 30,535,503 |
Total number of alignments: | 64,933,637 |
Number of secondary alignments: | 3,840,814 |
Number of non-unique alignments: | 6,333,335 |
Aligned to genes: | 50,371,200 |
Ambiguous alignments: | 183,892 |
No feature assigned: | 7,778,469 |
Missing chromosome in annotation: | 266,741 |
Not aligned: | 1,655,197 |
Reads genomic origin
Exonic: | 50,371,200 / 86.62% |
Intronic: | 5,613,385 / 9.65% |
Intergenic: | 2,165,084 / 3.72% |
Intronic/intergenic overlapping exon: | 1,936,644 / 3.33% |
Transcript coverage profile
5' bias: | 0.34 |
3' bias: | 0.19 |
5'-3' bias: | 2.01 |
Junction analysis
Reads at junctions: | 16,041,365 |
ACCT | 5.33% |
AGGT | 4.68% |
ATCT | 3.58% |
AGGA | 3.56% |
TCCT | 3.4% |
GCCT | 3.24% |
AGCT | 2.75% |
CCCT | 2.41% |
AGGC | 2.37% |
AGAT | 2.29% |
TTCT | 2.17% |