BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234099.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 = 5,139,935 number of mapped reads = 4,863,570 (94.62%) number of supplementary alignments = 34,186 (0.67%) number of secondary alignments = 0 number of mapped bases = 315,681,738 bp number of sequenced bases = 315,556,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 647,454 duplication rate = 11.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9578 >>>>>>> ACTG content number of A's = 82,297,939 bp (26.08%) number of C's = 57,215,488 bp (18.13%) number of T's = 102,222,173 bp (32.39%) number of G's = 73,789,448 bp (23.38%) number of N's = 31,167 bp (0.01%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,727,090 number of insertions = 21,377 mapped reads with insertion percentage = 0.43% number of deletions = 72,429 mapped reads with deletion percentage = 1.47% homopolymer indels = 44.54% >>>>>>> Coverage mean coverageData = 0.102X std coverageData = 1.2107X There is a 7.42% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.15% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 21479529 0.08617643123143914 2.8589598995868717 chr2 243199373 9470943 0.03894312260418533 1.8493968112975987 chr3 198022430 30691870 0.15499188652517798 0.5144624990412735 chr4 191154276 14207027 0.07432230812351799 0.43189814844199687 chr5 180915260 21523872 0.11897211987534938 0.475513549552904 chr6 171115067 24444266 0.14285279741029466 0.8208793283519428 chr7 159138663 12893467 0.08102033005015255 1.3022838917027604 chr8 146364022 24368328 0.16649124331934526 1.3728105987854031 chr9 141213431 13636841 0.09656900836861615 0.7042686357332608 chr10 135534747 15344465 0.11321425198808982 0.7595144622120896 chr11 135006516 17445122 0.12921688905741407 0.9735650250148306 chr12 133851895 9851332 0.07359874882608125 0.3864383932184048 chr13 115169878 11440156 0.09933288285674836 0.4685792613292131 chr14 107349540 18011605 0.16778465003203555 0.5822910385734962 chr15 102531392 4945846 0.048237382752006334 0.3377219475215353 chr16 90354753 9924334 0.10983743157374355 0.5179879526575182 chr17 81195210 9788785 0.12055865118151675 0.5898096506525291 chr18 78077248 7566687 0.0969128292021768 1.7297368910979571 chr19 59128983 12038562 0.20359832672921163 1.542295045473176 chr20 63025520 6739766 0.10693709468799305 0.477296570966457 chr21 48129895 7480408 0.15542124079015754 0.547415161899421 chr22 51304566 3129954 0.06100731852989459 0.3109174565562308 chrMT 16571 229493 13.849073682940077 8.590058206140148 chrX 155270560 8328934 0.05364142436273818 0.47027969052527496 chrY 59373566 700146 0.011792217432249227 0.2695984142364737