BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124797.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 140,977 number of mapped reads = 134,586 (95.47%) number of supplementary alignments = 7,490 (5.31%) number of secondary alignments = 0 number of mapped bases = 17,414,389 bp number of sequenced bases = 17,394,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,859 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2094 >>>>>>> ACTG content number of A's = 5,028,096 bp (28.91%) number of C's = 3,375,300 bp (19.4%) number of T's = 5,020,753 bp (28.86%) number of G's = 3,970,750 bp (22.83%) number of N's = 0 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 243,878 number of insertions = 4,513 mapped reads with insertion percentage = 3.07% number of deletions = 8,841 mapped reads with deletion percentage = 6.23% homopolymer indels = 43.07% >>>>>>> Coverage mean coverageData = 0.0056X std coverageData = 1.2541X There is a 0.46% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% 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 2625556 0.010533799231737922 4.172774307659727 chr2 243199373 1571126 0.006460238694776569 0.9284894344759107 chr3 198022430 1251652 0.006320758714050727 1.0038188262192942 chr4 191154276 864733 0.004523743952240963 0.3262546318543772 chr5 180915260 779160 0.004306767709921208 0.07121227908686167 chr6 171115067 785966 0.004593201602755414 0.0732083530034846 chr7 159138663 1065896 0.006697907220698468 0.08872600149953863 chr8 146364022 871746 0.005956012878629422 0.08534870108205508 chr9 141213431 598699 0.004239674624151013 0.07600198926310958 chr10 135534747 801677 0.005914918629685419 0.18438612533531362 chr11 135006516 585540 0.004337123994815183 0.06783950218043507 chr12 133851895 738202 0.0055150657373957985 0.13792943362888077 chr13 115169878 313670 0.0027235420011472097 0.05337337442880191 chr14 107349540 541411 0.00504344033518914 0.5110124571000015 chr15 102531392 467172 0.004556380157210779 0.15463008137427628 chr16 90354753 619713 0.006858665199383589 0.47298673314532486 chr17 81195210 477163 0.0058767382952762855 0.44399559649896625 chr18 78077248 233839 0.00299496980221434 0.06599188621990487 chr19 59128983 459824 0.007776626227445854 0.5090436906453236 chr20 63025520 405924 0.006440629129279695 0.09379311315771456 chr21 48129895 166727 0.0034641047939123907 0.08427637867570076 chr22 51304566 160934 0.0031368358130151614 0.058871694783255886 chrMT 16571 1348 0.08134693138615653 0.2754741503377927 chrX 155270560 662430 0.004266294911282603 0.06727924205263454 chrY 59373566 364281 0.0061354071271380265 0.1909627289773291