BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240258.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,578,306 number of mapped reads = 1,181,789 (74.88%) number of supplementary alignments = 4,413 (0.28%) number of secondary alignments = 0 number of mapped bases = 70,578,339 bp number of sequenced bases = 70,535,335 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,330 duplication rate = 5.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8413 >>>>>>> ACTG content number of A's = 18,952,691 bp (26.87%) number of C's = 11,793,111 bp (16.72%) number of T's = 22,256,413 bp (31.55%) number of G's = 17,517,638 bp (24.84%) number of N's = 15,482 bp (0.02%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 761,304 number of insertions = 5,305 mapped reads with insertion percentage = 0.45% number of deletions = 25,066 mapped reads with deletion percentage = 2.09% homopolymer indels = 49.82% >>>>>>> Coverage mean coverageData = 0.0228X std coverageData = 0.2715X There is a 1.86% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 5021985 0.020148334956405185 0.3096444757618863 chr2 243199373 7385939 0.030369893264486334 0.3407917638442766 chr3 198022430 5153712 0.02602590019726553 0.20184707545602637 chr4 191154276 4959001 0.025942401623283592 0.21137436332793721 chr5 180915260 3689606 0.020394111585722508 0.17804639831975153 chr6 171115067 4048071 0.023657010869767535 0.22296430093958125 chr7 159138663 4190133 0.026330075426108112 0.6013590478760052 chr8 146364022 4274583 0.029205148516621114 0.30524053635324455 chr9 141213431 2512189 0.01779001460562204 0.2390401835665456 chr10 135534747 2806438 0.020706409700237238 0.20817122742115757 chr11 135006516 3261340 0.024156908100643082 0.25760307224543855 chr12 133851895 3115837 0.023278243464539668 0.1878128820526704 chr13 115169878 1649874 0.014325568704692038 0.14550816109522854 chr14 107349540 2501205 0.023299634073886112 0.19895377038619214 chr15 102531392 1825827 0.017807492557986533 0.20542637037225076 chr16 90354753 1845575 0.0204258762126216 0.17635949731459932 chr17 81195210 2028958 0.024988641571343926 0.20731805608145992 chr18 78077248 1595858 0.020439475530694935 0.37993459649143924 chr19 59128983 1304410 0.022060416631890997 0.25713812792422214 chr20 63025520 1369623 0.021731244740225863 0.19362918240767218 chr21 48129895 1086971 0.02258411326266139 0.18817814403295974 chr22 51304566 670755 0.013073982537928495 0.1376781962135552 chrMT 16571 51513 3.108623498883592 4.309346809613977 chrX 155270560 4055806 0.026120895036380366 0.22689257189884587 chrY 59373566 173130 0.002915944108864878 0.06750947957077023