BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234130.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 = 3,394,099 number of mapped reads = 2,929,547 (86.31%) number of supplementary alignments = 29,612 (0.87%) number of secondary alignments = 0 number of mapped bases = 201,131,422 bp number of sequenced bases = 201,065,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 762,535 duplication rate = 10.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0751 >>>>>>> ACTG content number of A's = 48,326,323 bp (24.04%) number of C's = 33,537,674 bp (16.68%) number of T's = 51,721,052 bp (25.72%) number of G's = 67,440,981 bp (33.54%) number of N's = 39,829 bp (0.02%) GC percentage = 50.22% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,321,402 number of insertions = 13,825 mapped reads with insertion percentage = 0.47% number of deletions = 39,549 mapped reads with deletion percentage = 1.34% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.065X std coverageData = 60.5378X There is a 2.13% of reference with a coverageData >= 1X There is a 1.19% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 18450977 0.07402580152448246 0.6647292006198888 chr2 243199373 34328087 0.14115203742733334 215.96992116457375 chr3 198022430 3294016 0.016634560034436502 0.2691202043282576 chr4 191154276 5889980 0.03081270334753066 0.37172255381638114 chr5 180915260 14020197 0.07749593373162662 0.5975286153754324 chr6 171115067 28797371 0.16829243330162152 1.3921856732821907 chr7 159138663 9705309 0.06098649326970907 0.7880249385895179 chr8 146364022 8634312 0.05899203835762316 0.7635596984649944 chr9 141213431 4056345 0.028724923481251583 0.6596599358204402 chr10 135534747 1989302 0.014677431758514294 0.2700153271163969 chr11 135006516 1595439 0.011817496275513102 0.4575754718305104 chr12 133851895 4178974 0.031220880361835745 0.9674296746148726 chr13 115169878 16617399 0.1442859824858024 0.8310601527028043 chr14 107349540 17206269 0.16028265235230632 0.9534510333202469 chr15 102531392 1582338 0.015432717425703145 0.9974797034014624 chr16 90354753 1890689 0.02092517479406977 0.4359407143988595 chr17 81195210 3539658 0.04359441893185571 0.41685088624897615 chr18 78077248 6476527 0.08295024691444043 1.7982922900092901 chr19 59128983 2281073 0.038577917025902506 0.4882776971155887 chr20 63025520 6051507 0.09601677225352524 0.7265540878880855 chr21 48129895 4021066 0.0835461203478628 0.6687336760261758 chr22 51304566 2939306 0.057291313993378286 0.5382412565749947 chrMT 16571 101536 6.127330879246877 6.547901766680769 chrX 155270560 2131922 0.013730368461349016 0.32821127820422535 chrY 59373566 1351823 0.022768095148605356 0.41175280647637785