BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156415.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,608,694 number of mapped reads = 6,476,483 (98%) number of supplementary alignments = 848,521 (12.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,239,974 number of mapped paired reads (second in pair) = 3,236,509 number of mapped paired reads (both in pair) = 6,393,170 number of mapped paired reads (singletons) = 83,313 number of mapped bases = 732,985,250 bp number of sequenced bases = 732,446,724 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,171,527 duplication rate = 64.97% >>>>>>> Insert size mean insert size = 1,277,169.5648 std insert size = 9,400,645.0661 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.5681 >>>>>>> ACTG content number of A's = 219,471,687 bp (29.96%) number of C's = 144,815,047 bp (19.77%) number of T's = 217,716,759 bp (29.72%) number of G's = 150,437,488 bp (20.54%) number of N's = 5,743 bp (0%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 6,173,658 number of insertions = 80,749 mapped reads with insertion percentage = 1.2% number of deletions = 224,171 mapped reads with deletion percentage = 3.38% homopolymer indels = 40.93% >>>>>>> Coverage mean coverageData = 0.2368X std coverageData = 4.4423X There is a 5.11% of reference with a coverageData >= 1X There is a 3.82% of reference with a coverageData >= 2X There is a 2.83% of reference with a coverageData >= 3X There is a 2.28% of reference with a coverageData >= 4X There is a 1.7% of reference with a coverageData >= 5X There is a 1.42% of reference with a coverageData >= 6X There is a 1.06% of reference with a coverageData >= 7X There is a 0.92% of reference with a coverageData >= 8X There is a 0.69% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.42% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 58392353 0.23427164500424655 2.006355322747997 chr2 243199373 63646065 0.2617032446049933 14.547237013873282 chr3 198022430 55272391 0.27912187018409984 1.5948236570429608 chr4 191154276 50473416 0.264045445679698 2.132877890252889 chr5 180915260 40010311 0.2211549816195715 1.4107461670491075 chr6 171115067 40241144 0.2351700800257408 1.6473700479008873 chr7 159138663 40972667 0.25746519561999837 1.917366324828242 chr8 146364022 38198034 0.2609796688970463 2.4845528521941436 chr9 141213431 33165789 0.23486285097059925 1.9221317010989944 chr10 135534747 32495962 0.23976111454282642 2.6483539464924735 chr11 135006516 34991925 0.25918693435507956 1.5825832741616894 chr12 133851895 33994390 0.2539701809974375 1.5649911737519238 chr13 115169878 25054167 0.2175409702179245 1.4086622760681164 chr14 107349540 23069460 0.21490040851595638 1.3997561712882882 chr15 102531392 22361957 0.21809863851258354 1.4295028813320785 chr16 90354753 23673157 0.2620023431418157 2.1046569007368743 chr17 81195210 20259007 0.24950987872314143 1.6579875652514318 chr18 78077248 22445697 0.28748063712491506 2.689834752791848 chr19 59128983 13404234 0.22669481732841573 1.6457764150781773 chr20 63025520 14526069 0.23047916145713673 1.5083414553265013 chr21 48129895 10831606 0.22504944172431707 1.8116878334275697 chr22 51304566 8949296 0.1744346887175695 1.528493188380385 chrMT 16571 750739 45.304387182427135 46.81757723933082 chrX 155270560 20331278 0.13094097168194666 1.0880755609294501 chrY 59373566 5474136 0.09219820146898369 1.414778446856271