Input data and parameters
Input
Analysis date: | Sun Oct 29 01:43:01 GMT 2023 |
BAM file: | SRX7354059.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): | 32,044,222 / 32,024,451 |
Number of aligned pairs (without duplicates): | 32,020,437 |
Total number of alignments: | 68,564,599 |
Number of secondary alignments: | 4,495,926 |
Number of non-unique alignments: | 6,961,804 |
Aligned to genes: | 48,844,279 |
Ambiguous alignments: | 202,013 |
No feature assigned: | 12,065,261 |
Missing chromosome in annotation: | 491,242 |
Not aligned: | 1,752,511 |
Reads genomic origin
Exonic: | 48,844,279 / 80.19% |
Intronic: | 10,083,901 / 16.56% |
Intergenic: | 1,981,360 / 3.25% |
Intronic/intergenic overlapping exon: | 2,411,238 / 3.96% |
Transcript coverage profile
5' bias: | 0.39 |
3' bias: | 0.22 |
5'-3' bias: | 1.93 |
Junction analysis
Reads at junctions: | 18,129,667 |
ACCT | 5.34% |
AGGT | 4.59% |
ATCT | 3.62% |
TCCT | 3.56% |
AGGA | 3.48% |
GCCT | 3.06% |
AGCT | 2.77% |
AGGC | 2.46% |
CCCT | 2.42% |
AGAT | 2.24% |
TTCT | 2.13% |