Input data and parameters
Input
Analysis date: | Mon Oct 30 22:25:44 GMT 2023 |
BAM file: | SRX7354263.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): | 31,739,100 / 31,702,146 |
Number of aligned pairs (without duplicates): | 31,691,248 |
Total number of alignments: | 67,886,239 |
Number of secondary alignments: | 4,444,993 |
Number of non-unique alignments: | 7,157,317 |
Aligned to genes: | 54,084,209 |
Ambiguous alignments: | 182,103 |
No feature assigned: | 6,010,572 |
Missing chromosome in annotation: | 452,038 |
Not aligned: | 5,614,372 |
Reads genomic origin
Exonic: | 54,084,209 / 90% |
Intronic: | 3,363,418 / 5.6% |
Intergenic: | 2,647,154 / 4.4% |
Intronic/intergenic overlapping exon: | 2,202,253 / 3.66% |
Transcript coverage profile
5' bias: | 0.33 |
3' bias: | 0.19 |
5'-3' bias: | 2.13 |
Junction analysis
Reads at junctions: | 17,883,484 |
ACCT | 5.44% |
AGGT | 4.66% |
ATCT | 3.62% |
TCCT | 3.58% |
AGGA | 3.43% |
GCCT | 3.12% |
AGCT | 2.69% |
AGGC | 2.4% |
CCCT | 2.36% |
TTCT | 2.24% |
AGAT | 2.18% |