BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818818.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,247,182 number of mapped reads = 3,159,983 (97.31%) number of supplementary alignments = 27,152 (0.84%) number of secondary alignments = 0 number of mapped bases = 214,821,275 bp number of sequenced bases = 214,735,362 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,122,310 duplication rate = 50.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1414 >>>>>>> ACTG content number of A's = 63,914,512 bp (29.76%) number of C's = 44,796,779 bp (20.86%) number of T's = 60,115,010 bp (27.99%) number of G's = 45,896,236 bp (21.37%) number of N's = 12,825 bp (0.01%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,092,767 number of insertions = 28,340 mapped reads with insertion percentage = 0.89% number of deletions = 54,727 mapped reads with deletion percentage = 1.72% homopolymer indels = 39.95% >>>>>>> Coverage mean coverageData = 0.0694X std coverageData = 0.9392X There is a 1.79% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 17817373 0.07148376573152049 1.170461419350164 chr2 243199373 18792134 0.07727048704192177 1.481118547096239 chr3 198022430 14922089 0.07535554936882655 0.7857475749561593 chr4 191154276 14021494 0.07335171513505667 0.8331448249038331 chr5 180915260 13551533 0.07490541704442179 0.8023749382649592 chr6 171115067 12978021 0.07584382385216844 0.8294139729048063 chr7 159138663 11729205 0.07370430779602566 0.8656541943409642 chr8 146364022 11109511 0.07590329131567593 0.8523721114766972 chr9 141213431 9159320 0.06486153572743375 0.7937494155934123 chr10 135534747 10292358 0.07593888820259502 0.9638944423234027 chr11 135006516 10291282 0.07622803924515761 0.8495681513782781 chr12 133851895 9825924 0.07340892708317652 0.8010374812499139 chr13 115169878 6795007 0.05899986279398507 0.6988099491513934 chr14 107349540 6656054 0.06200356331289356 0.7686026255696509 chr15 102531392 6084692 0.0593446736780868 0.6962040272448237 chr16 90354753 6283472 0.06954224090458197 0.9747641694870032 chr17 81195210 5676869 0.06991630417607148 0.7960784597606417 chr18 78077248 5859577 0.0750484571382434 0.9344369363228588 chr19 59128983 4105511 0.06943314076617892 1.0134289159354795 chr20 63025520 4769988 0.0756834374393103 0.8382717571872287 chr21 48129895 2832002 0.05884080985424963 0.7124653541292917 chr22 51304566 2731058 0.05323226006823642 0.7229190318671128 chrMT 16571 151435 9.138555307464848 11.027521556092923 chrX 155270560 6390889 0.04115969569504998 0.6020644582636225 chrY 59373566 1994477 0.0335920028788569 1.597598281828194