BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084886.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,539,412 number of mapped reads = 2,279,817 (89.78%) number of supplementary alignments = 16,129 (0.64%) number of secondary alignments = 0 number of mapped bases = 158,892,399 bp number of sequenced bases = 158,828,105 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,249 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9608 >>>>>>> ACTG content number of A's = 46,580,093 bp (29.33%) number of C's = 29,110,496 bp (18.33%) number of T's = 50,910,691 bp (32.05%) number of G's = 32,201,528 bp (20.27%) number of N's = 25,297 bp (0.02%) GC percentage = 38.6% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,312,147 number of insertions = 12,734 mapped reads with insertion percentage = 0.55% number of deletions = 36,502 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.98% >>>>>>> Coverage mean coverageData = 0.0513X std coverageData = 0.4368X There is a 4.29% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12604598 0.050569976313118194 0.718504881283705 chr2 243199373 13675112 0.05623004628387755 0.47509795734373356 chr3 198022430 11668991 0.058927622492058095 0.2779064043963773 chr4 191154276 10243574 0.05358799297798601 0.26913033993629026 chr5 180915260 9002136 0.04975885395184464 0.26401673169386963 chr6 171115067 9233031 0.05395802463146042 0.2738774124230602 chr7 159138663 10014981 0.062932418880508 0.4045462898932369 chr8 146364022 8615566 0.05886396043421108 0.9880700151840228 chr9 141213431 10912113 0.07727390321675563 0.45396183826379805 chr10 135534747 5056698 0.037309237018017236 0.2843348135486286 chr11 135006516 7151704 0.05297302835368332 0.36139538854800457 chr12 133851895 7336250 0.054808712271126235 0.27501806861905 chr13 115169878 4502941 0.03909825275668 0.2245093703059543 chr14 107349540 3455192 0.032186369871729306 0.2258046890990868 chr15 102531392 3603751 0.035147781861773614 0.2144204710450702 chr16 90354753 2878365 0.031856265491644914 0.23645558440290024 chr17 81195210 3860976 0.047551770603216616 0.26391602549723203 chr18 78077248 7082843 0.09071583824265937 0.8189436809007231 chr19 59128983 3281260 0.05549325954075686 0.4439724960183434 chr20 63025520 2840877 0.045075026751068455 0.2589971215389512 chr21 48129895 1467472 0.030489823424713475 0.2156834744429891 chr22 51304566 1385932 0.027013813936170906 0.18391957527496053 chrMT 16571 64450 3.8893247239152737 2.621606144306007 chrX 155270560 8594273 0.05535030594338038 0.30277937831849694 chrY 59373566 359313 0.006051733527341107 0.1698570143454056