BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238487.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 = 2,974,823 number of mapped reads = 2,551,710 (85.78%) number of supplementary alignments = 20,784 (0.7%) number of secondary alignments = 0 number of mapped bases = 154,866,476 bp number of sequenced bases = 154,783,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 752,509 duplication rate = 21.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6847 >>>>>>> ACTG content number of A's = 37,760,782 bp (24.4%) number of C's = 26,723,170 bp (17.26%) number of T's = 52,262,841 bp (33.77%) number of G's = 38,026,013 bp (24.57%) number of N's = 10,244 bp (0.01%) GC percentage = 41.83% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 942,313 number of insertions = 9,391 mapped reads with insertion percentage = 0.36% number of deletions = 49,405 mapped reads with deletion percentage = 1.92% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.05X std coverageData = 0.6722X There is a 2.39% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 17259250 0.06924456168155345 1.0906609022755924 chr2 243199373 11822768 0.04861348059478755 1.3578776474296546 chr3 198022430 15403175 0.07778500142635357 0.5302993779675846 chr4 191154276 12093620 0.06326628026882328 0.4680599964444174 chr5 180915260 8635408 0.04773178337747739 0.4092550829262637 chr6 171115067 8803775 0.05144944366588128 0.6199335138228939 chr7 159138663 7906290 0.04968176715170719 0.5612766991942808 chr8 146364022 3884005 0.026536610206024536 0.6042089491956383 chr9 141213431 3213051 0.022753154407812667 0.3345621092931242 chr10 135534747 6026777 0.04446665621473437 0.4762571885272727 chr11 135006516 11928845 0.08835755009039711 0.5901011799701661 chr12 133851895 4549628 0.03399001560642828 0.3503822891355941 chr13 115169878 3945179 0.034255302415098506 0.4248461127262582 chr14 107349540 2957378 0.02754905144446823 0.31651813163719267 chr15 102531392 5522801 0.053864488643634134 0.5121728782106079 chr16 90354753 3312632 0.036662509608099976 0.37468740793416627 chr17 81195210 2161384 0.026619599850779375 0.32051160768586107 chr18 78077248 10878342 0.139327938402747 1.1036760744175957 chr19 59128983 3620002 0.061222125197045923 0.7115257263559205 chr20 63025520 2397171 0.038034926169589714 0.36508950216732694 chr21 48129895 2180728 0.04530921997648239 0.3992786593445258 chr22 51304566 908930 0.017716356863831575 0.2465522266153952 chrMT 16571 30489 1.8399010319232394 2.535723579566249 chrX 155270560 5062549 0.03260469338166875 0.34128717652115753 chrY 59373566 362299 0.006102025268281848 0.22573159597947762