BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1781822.sorted.bam
outfile = /home/yangyx/scDNA/SRP052954/SRP052954.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 386,387,256
number of mapped reads = 366,552,220 (94.87%)
number of supplementary alignments = 1,344,452 (0.35%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 188,197,058
number of mapped paired reads (second in pair) = 178,355,162
number of mapped paired reads (both in pair) = 354,670,002
number of mapped paired reads (singletons) = 11,882,218
number of mapped bases = 35,547,005,515 bp
number of sequenced bases = 35,539,829,371 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 42,062,171
duplication rate = 11.04%
>>>>>>> Insert size
mean insert size = 44,804.7565
std insert size = 2,057,358.8659
median insert size = 207
>>>>>>> Mapping quality
mean mapping quality = 53.7028
>>>>>>> ACTG content
number of A's = 10,408,371,866 bp (29.29%)
number of C's = 7,285,179,098 bp (20.5%)
number of T's = 10,363,669,559 bp (29.16%)
number of G's = 7,383,248,836 bp (20.77%)
number of N's = 99,360,012 bp (0.28%)
GC percentage = 41.27%
>>>>>>> Mismatches and indels
general error rate = 0.0063
number of mismatches = 216,660,384
number of insertions = 3,204,490
mapped reads with insertion percentage = 0.86%
number of deletions = 3,167,660
mapped reads with deletion percentage = 0.85%
homopolymer indels = 45.7%
>>>>>>> Coverage
mean coverageData = 11.4827X
std coverageData = 13.357X
There is a 89.71% of reference with a coverageData >= 1X
There is a 86.69% of reference with a coverageData >= 2X
There is a 82.68% of reference with a coverageData >= 3X
There is a 77.92% of reference with a coverageData >= 4X
There is a 72.67% of reference with a coverageData >= 5X
There is a 67.2% of reference with a coverageData >= 6X
There is a 61.7% of reference with a coverageData >= 7X
There is a 56.33% of reference with a coverageData >= 8X
There is a 51.21% of reference with a coverageData >= 9X
There is a 46.41% of reference with a coverageData >= 10X
There is a 41.95% of reference with a coverageData >= 11X
There is a 37.86% of reference with a coverageData >= 12X
There is a 34.13% of reference with a coverageData >= 13X
There is a 30.76% of reference with a coverageData >= 14X
There is a 27.7% of reference with a coverageData >= 15X
There is a 24.96% of reference with a coverageData >= 16X
There is a 22.49% of reference with a coverageData >= 17X
There is a 20.27% of reference with a coverageData >= 18X
There is a 18.29% of reference with a coverageData >= 19X
There is a 16.52% of reference with a coverageData >= 20X
There is a 14.93% of reference with a coverageData >= 21X
There is a 13.5% of reference with a coverageData >= 22X
There is a 12.23% of reference with a coverageData >= 23X
There is a 11.08% of reference with a coverageData >= 24X
There is a 10.05% of reference with a coverageData >= 25X
There is a 9.13% of reference with a coverageData >= 26X
There is a 8.3% of reference with a coverageData >= 27X
There is a 7.56% of reference with a coverageData >= 28X
There is a 6.89% of reference with a coverageData >= 29X
There is a 6.28% of reference with a coverageData >= 30X
There is a 5.74% of reference with a coverageData >= 31X
There is a 5.24% of reference with a coverageData >= 32X
There is a 4.8% of reference with a coverageData >= 33X
There is a 4.4% of reference with a coverageData >= 34X
There is a 4.03% of reference with a coverageData >= 35X
There is a 3.7% of reference with a coverageData >= 36X
There is a 3.4% of reference with a coverageData >= 37X
There is a 3.13% of reference with a coverageData >= 38X
There is a 2.88% of reference with a coverageData >= 39X
There is a 2.65% of reference with a coverageData >= 40X
There is a 2.44% of reference with a coverageData >= 41X
There is a 2.26% of reference with a coverageData >= 42X
There is a 2.08% of reference with a coverageData >= 43X
There is a 1.93% of reference with a coverageData >= 44X
There is a 1.78% of reference with a coverageData >= 45X
There is a 1.65% of reference with a coverageData >= 46X
There is a 1.53% of reference with a coverageData >= 47X
There is a 1.42% of reference with a coverageData >= 48X
There is a 1.32% of reference with a coverageData >= 49X
There is a 1.23% of reference with a coverageData >= 50X
There is a 1.14% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 2845174970 11.414916274170487 17.75984051823788
chr2 243199373 2904604053 11.943304035574137 14.707258095872685
chr3 198022430 2419359891 12.217605303601212 10.789377890111512
chr4 191154276 2231091364 11.671679078735336 11.788580288789145
chr5 180915260 2113664008 11.683171491448539 9.92083308850688
chr6 171115067 2058290639 12.028693177556363 11.618098656546533
chr7 159138663 1819974966 11.436409805705104 12.03356022309483
chr8 146364022 1760890897 12.030899895604126 11.120490705195307
chr9 141213431 1431452162 10.136798970630492 13.420327528973067
chr10 135534747 1949319302 14.382432144872784 20.069504435268424
chr11 135006516 1612454260 11.943529155289069 11.210364761354084
chr12 133851895 2360218688 17.633061437045775 15.704260394290115
chr13 115169878 1086967614 9.437950555092192 9.702347703025916
chr14 107349540 1055809474 9.835249168277759 10.663571674391402
chr15 102531392 1002150792 9.774087452162943 10.722899166650825
chr16 90354753 884356165 9.787599828865671 11.078611330587645
chr17 81195210 793034030 9.767005097960828 11.515847241585535
chr18 78077248 883614122 11.317178110580947 13.70309955697735
chr19 59128983 535384393 9.05451718998786 13.405918246493535
chr20 63025520 696097285 11.044689278247922 12.551300717123361
chr21 48129895 417788486 8.680436265235983 16.803346183245328
chr22 51304566 349736822 6.816875168576614 9.905263580124416
chrMT 16571 2028602 122.41880393458452 35.09041880440738
chrX 155270560 2299396468 14.808966155593179 13.264820245439344
chrY 59373566 34146062 0.5751054602312416 6.317522055849752