BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751218.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 6,182,653 number of mapped reads = 4,995,816 (80.8%) number of supplementary alignments = 304,536 (4.93%) number of secondary alignments = 0 number of mapped bases = 490,539,343 bp number of sequenced bases = 490,376,745 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,155 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.8459 >>>>>>> ACTG content number of A's = 143,657,871 bp (29.3%) number of C's = 101,339,422 bp (20.67%) number of T's = 144,681,253 bp (29.5%) number of G's = 100,694,637 bp (20.53%) number of N's = 3,562 bp (0%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,806,352 number of insertions = 427,727 mapped reads with insertion percentage = 8.16% number of deletions = 76,270 mapped reads with deletion percentage = 1.5% homopolymer indels = 53.95% >>>>>>> Coverage mean coverageData = 0.1585X std coverageData = 1.4156X There is a 12.62% of reference with a coverageData >= 1X There is a 2.24% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% 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 61058552 0.24496850501327336 3.6161045168780572 chr2 243199373 36738614 0.151063769395491 0.6875906508739561 chr3 198022430 33087304 0.16708866768274686 0.6307141283698332 chr4 191154276 21010641 0.10991457496875456 0.44364944783804855 chr5 180915260 38425293 0.21239387434758128 0.542807142029183 chr6 171115067 27811271 0.16252964445264192 1.0377899579893155 chr7 159138663 26757925 0.168142200616578 0.9123241953823814 chr8 146364022 23074583 0.1576520150559951 0.6168813590358305 chr9 141213431 22119349 0.1566377138729814 0.8493436684316963 chr10 135534747 25861606 0.19081163002429186 2.8409641339761547 chr11 135006516 22522832 0.16682774037365722 0.7321690362930742 chr12 133851895 26784777 0.20010756665043852 0.5179499907798601 chr13 115169878 12961014 0.11253822809467594 0.37891940144849806 chr14 107349540 10871466 0.10127165891907874 0.3801894796383916 chr15 102531392 12648855 0.12336568101991632 0.39855552498755603 chr16 90354753 14159564 0.15671078199948152 1.3977992465844935 chr17 81195210 14497208 0.17854757688292203 0.7481600489366799 chr18 78077248 9972475 0.1277257492477194 1.4903277212319936 chr19 59128983 9429419 0.15947203083130992 2.5196857437793176 chr20 63025520 9088687 0.14420645795544407 0.4419777572372445 chr21 48129895 4155021 0.08632931777640487 0.38122126393268924 chr22 51304566 5972069 0.11640423973180086 0.39172479373701824 chrMT 16571 1043885 62.994689517832356 24.049488421217227 chrX 155270560 19500511 0.12559052405040594 0.4825497260694698 chrY 59373566 986422 0.016613824407986543 0.5740401348548704