BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173941.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 = 3,225,956 number of mapped reads = 3,150,844 (97.67%) number of supplementary alignments = 421,169 (13.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,578,202 number of mapped paired reads (second in pair) = 1,572,642 number of mapped paired reads (both in pair) = 3,106,112 number of mapped paired reads (singletons) = 44,732 number of mapped bases = 350,843,760 bp number of sequenced bases = 350,593,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,461,223 duplication rate = 61.52% >>>>>>> Insert size mean insert size = 1,016,235.0954 std insert size = 9,597,519.2275 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 52.5355 >>>>>>> ACTG content number of A's = 105,041,055 bp (29.96%) number of C's = 69,388,172 bp (19.79%) number of T's = 104,115,891 bp (29.7%) number of G's = 72,045,759 bp (20.55%) number of N's = 2,997 bp (0%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 3,017,504 number of insertions = 40,444 mapped reads with insertion percentage = 1.23% number of deletions = 107,128 mapped reads with deletion percentage = 3.32% homopolymer indels = 40.57% >>>>>>> Coverage mean coverageData = 0.1133X std coverageData = 2.2646X There is a 2.62% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 1.32% of reference with a coverageData >= 3X There is a 1.06% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.66% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% 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 28184568 0.1130772227845322 1.2573698091512535 chr2 243199373 33655009 0.13838443983159446 7.064713811049938 chr3 198022430 24651295 0.12448738761563526 1.0642255202223674 chr4 191154276 23520809 0.12304620902124104 1.3253744218340247 chr5 180915260 20570533 0.11370258650375872 1.0014882207864235 chr6 171115067 20731396 0.1211547081356664 1.0839982962357948 chr7 159138663 20447638 0.1284894419403285 1.2764602717053943 chr8 146364022 18471875 0.12620502462005315 1.528717175011265 chr9 141213431 15822364 0.1120457444306413 1.1260780090518634 chr10 135534747 17297336 0.1276228892064114 1.4560303027231594 chr11 135006516 16237177 0.12026958017344881 1.0520749497141413 chr12 133851895 16487276 0.12317551425028386 1.0686063625425921 chr13 115169878 9995523 0.08678938602331418 0.8768161660240029 chr14 107349540 6767811 0.06304462040545307 0.7551513304499731 chr15 102531392 9905295 0.09660743706668881 0.9225092703011408 chr16 90354753 10961350 0.12131459205029314 1.1324286176934206 chr17 81195210 9919506 0.1221686106852855 1.051546356747098 chr18 78077248 10428041 0.13356056043368741 1.4275346390580592 chr19 59128983 6345667 0.10731906212559077 1.0547644639818115 chr20 63025520 7796519 0.12370415983874469 1.1165541119772804 chr21 48129895 5193523 0.10790638541804423 1.1150055219744994 chr22 51304566 4557113 0.08882470616747835 0.9921418081847181 chrMT 16571 555746 33.537263894755895 29.925116762254362 chrX 155270560 9240531 0.05951244717607768 0.7195216987258758 chrY 59373566 3099859 0.05220941251869561 1.0016649962033533