BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237601.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 = 2,509,773 number of mapped reads = 1,844,192 (73.48%) number of supplementary alignments = 8,777 (0.35%) number of secondary alignments = 0 number of mapped bases = 111,091,376 bp number of sequenced bases = 111,032,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,990 duplication rate = 4.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1203 >>>>>>> ACTG content number of A's = 29,786,074 bp (26.83%) number of C's = 20,904,928 bp (18.83%) number of T's = 32,524,506 bp (29.29%) number of G's = 27,627,232 bp (24.88%) number of N's = 189,852 bp (0.17%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 1,139,554 number of insertions = 9,721 mapped reads with insertion percentage = 0.52% number of deletions = 36,680 mapped reads with deletion percentage = 1.96% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.3159X There is a 2.81% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.04% 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% 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 9597138 0.038503968260925614 0.37891026925726434 chr2 243199373 9245377 0.038015628436673644 0.4391015338176891 chr3 198022430 7591545 0.038336793463245554 0.26953586883084674 chr4 191154276 7185189 0.03758842935849366 0.27191730954005167 chr5 180915260 6327582 0.03497539124118109 0.243600355584857 chr6 171115067 5651943 0.033030072097625394 0.268704140334714 chr7 159138663 6598615 0.041464562260398026 0.4217019358199329 chr8 146364022 5755178 0.03932098832320965 0.3305796637815731 chr9 141213431 4473717 0.031680534693615654 0.3244107493936335 chr10 135534747 5270679 0.038888027732106215 0.3182078072883245 chr11 135006516 4735002 0.035072396061239 0.3154146003802466 chr12 133851895 6847757 0.05115920846694027 0.3178837576491732 chr13 115169878 3548856 0.030814098804550265 0.24225353480427056 chr14 107349540 3227924 0.030069285811564726 0.251818247950164 chr15 102531392 3610281 0.03521146967360006 0.26860859931748815 chr16 90354753 2956399 0.03271990572538005 0.2727089320273837 chr17 81195210 2761549 0.03401123046544248 0.2573156713414608 chr18 78077248 2852957 0.036540183895825834 0.41085632834840546 chr19 59128983 2203943 0.0372734805873458 0.3142048123703306 chr20 63025520 2242326 0.03557806425079872 0.2614611491736604 chr21 48129895 1319322 0.02741169495591046 0.2445037255894449 chr22 51304566 1175858 0.022919168636959135 0.2089377254048128 chrMT 16571 81384 4.911230462856798 4.118716551879235 chrX 155270560 5456675 0.03514301101251905 0.2676083883890626 chrY 59373566 374180 0.006302131153786518 0.14760857087631532