BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237826.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 = 2,590,817 number of mapped reads = 2,479,993 (95.72%) number of supplementary alignments = 15,277 (0.59%) number of secondary alignments = 0 number of mapped bases = 181,377,535 bp number of sequenced bases = 181,299,175 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,359 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9855 >>>>>>> ACTG content number of A's = 54,590,149 bp (30.11%) number of C's = 36,018,918 bp (19.87%) number of T's = 54,279,395 bp (29.94%) number of G's = 36,089,906 bp (19.91%) number of N's = 320,807 bp (0.18%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,602,795 number of insertions = 15,746 mapped reads with insertion percentage = 0.63% number of deletions = 41,919 mapped reads with deletion percentage = 1.67% homopolymer indels = 46.81% >>>>>>> Coverage mean coverageData = 0.0586X std coverageData = 0.6736X There is a 3.94% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 13965714 0.05603080924721147 1.4435273669685167 chr2 243199373 10915008 0.04488090518226789 0.6206924915663657 chr3 198022430 18660441 0.0942339764237819 0.43924426779953407 chr4 191154276 8877302 0.046440509654097406 0.3845196647437735 chr5 180915260 10968654 0.06062868328520214 0.3432285804592851 chr6 171115067 8743726 0.051098516064631526 0.4086376887307943 chr7 159138663 14092770 0.0885565439242128 0.8801982107948739 chr8 146364022 13131306 0.08971676113136601 0.6872027533757478 chr9 141213431 6214006 0.044004355364752806 0.535567590836578 chr10 135534747 1528783 0.011279638866334402 0.7853009395597574 chr11 135006516 8814055 0.0652861451516903 0.6741335028929796 chr12 133851895 6443791 0.0481412011387661 0.31527269871278624 chr13 115169878 4540414 0.039423624291761425 0.2692157092938836 chr14 107349540 8270738 0.07704493191121266 0.3991785187996513 chr15 102531392 3288194 0.03207011955909074 0.24113904423375285 chr16 90354753 7111781 0.07870953949705335 0.4818462810118622 chr17 81195210 5980082 0.07365067471344676 0.6300778837070082 chr18 78077248 7254653 0.09291635125254415 1.0993396136639797 chr19 59128983 3172896 0.053660588074041456 0.8943021516743516 chr20 63025520 4151741 0.06587396660908153 0.371444210656041 chr21 48129895 786637 0.016344041473599726 0.31166650162689086 chr22 51304566 1402477 0.027336299852921474 0.222600631530687 chrMT 16571 17947 1.083036630257679 1.3285578416800812 chrX 155270560 12475161 0.08034466417845083 0.4498312018079266 chrY 59373566 569258 0.009587734716826677 0.3882761984580386