Input data and parameters
Input
Analysis date: | Sun Oct 29 11:54:05 GMT 2023 |
BAM file: | SRX7354092.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): | 41,736,374 / 41,709,084 |
Number of aligned pairs (without duplicates): | 41,704,046 |
Total number of alignments: | 89,927,303 |
Number of secondary alignments: | 6,481,845 |
Number of non-unique alignments: | 10,382,599 |
Aligned to genes: | 65,579,389 |
Ambiguous alignments: | 270,606 |
No feature assigned: | 13,085,651 |
Missing chromosome in annotation: | 609,058 |
Not aligned: | 4,842,098 |
Reads genomic origin
Exonic: | 65,579,389 / 83.37% |
Intronic: | 8,763,168 / 11.14% |
Intergenic: | 4,322,483 / 5.49% |
Intronic/intergenic overlapping exon: | 2,638,502 / 3.35% |
Transcript coverage profile
5' bias: | 0.5 |
3' bias: | 0.33 |
5'-3' bias: | 1.6 |
Junction analysis
Reads at junctions: | 24,128,720 |
ACCT | 5.09% |
AGGT | 4.68% |
TCCT | 3.64% |
AGGA | 3.43% |
ATCT | 3.34% |
GCCT | 3.19% |
AGCT | 2.79% |
CCCT | 2.55% |
AGGC | 2.42% |
AGAT | 2.21% |
TTCT | 2.17% |