BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238304.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 = 2,331,181 number of mapped reads = 2,143,053 (91.93%) number of supplementary alignments = 22,390 (0.96%) number of secondary alignments = 0 number of mapped bases = 142,885,512 bp number of sequenced bases = 142,822,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,345 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2294 >>>>>>> ACTG content number of A's = 40,685,946 bp (28.49%) number of C's = 26,693,148 bp (18.69%) number of T's = 44,762,675 bp (31.34%) number of G's = 30,633,389 bp (21.45%) number of N's = 47,253 bp (0.03%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,161,044 number of insertions = 10,547 mapped reads with insertion percentage = 0.49% number of deletions = 36,212 mapped reads with deletion percentage = 1.67% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.4211X There is a 3.85% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 12027346 0.04825402621564582 0.7276357617182586 chr2 243199373 12159651 0.0499986938699879 0.4427673373601852 chr3 198022430 9606486 0.04851211047152588 0.25267307196067307 chr4 191154276 9644838 0.05045577949823105 0.27423448699299197 chr5 180915260 9321985 0.05152680321162516 0.26554397487002884 chr6 171115067 8435257 0.049295816831839825 0.3069315212864705 chr7 159138663 7714931 0.04847930009315209 0.5385458853961944 chr8 146364022 7246516 0.04951022731528927 0.6899625921287298 chr9 141213431 5757904 0.040774478455948004 0.3679955281311475 chr10 135534747 6495042 0.04792160050293229 0.36902481879565663 chr11 135006516 6217936 0.04605656218845022 0.3460295670601352 chr12 133851895 6463696 0.04828991027732555 0.26465108747838995 chr13 115169878 4401958 0.03822143494846804 0.2276720362965806 chr14 107349540 4206972 0.03918947393719619 0.25815845076892385 chr15 102531392 4013179 0.03914097840396042 0.23216601741102372 chr16 90354753 3654037 0.040441004802481174 0.2546412838446371 chr17 81195210 3452460 0.04252048858547198 0.2643054460895497 chr18 78077248 3707292 0.0474823600340012 0.6586433003276763 chr19 59128983 2587849 0.04376616793831884 0.5236808243652394 chr20 63025520 2841281 0.045081436852881185 0.25079076920196636 chr21 48129895 1795040 0.03729573895808416 0.2466989938963893 chr22 51304566 1415605 0.027592183510528088 0.18904634812229154 chrMT 16571 596195 35.978214953835014 22.475963733590937 chrX 155270560 8775570 0.05651792587081543 0.30381449718820264 chrY 59373566 346486 0.005835694625449986 0.14805801280212977