BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237299.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 = 2,463,678 number of mapped reads = 1,958,252 (79.48%) number of supplementary alignments = 17,168 (0.7%) number of secondary alignments = 0 number of mapped bases = 117,365,878 bp number of sequenced bases = 117,298,955 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 736,156 duplication rate = 22.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0956 >>>>>>> ACTG content number of A's = 28,857,451 bp (24.6%) number of C's = 20,537,292 bp (17.51%) number of T's = 39,180,583 bp (33.4%) number of G's = 28,712,014 bp (24.48%) number of N's = 11,615 bp (0.01%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 835,299 number of insertions = 8,885 mapped reads with insertion percentage = 0.45% number of deletions = 38,728 mapped reads with deletion percentage = 1.95% homopolymer indels = 42.57% >>>>>>> Coverage mean coverageData = 0.0379X std coverageData = 0.6639X There is a 1.3% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 15810173 0.06343082691858168 0.7089826196146621 chr2 243199373 8231003 0.033844671959742265 1.3228584135399015 chr3 198022430 10615407 0.05360709390345326 0.5161829318579094 chr4 191154276 7003225 0.0366365071529972 0.5012570165539488 chr5 180915260 5613275 0.03102709522679292 0.4260812155336112 chr6 171115067 11886685 0.06946603363688598 0.7616591605758198 chr7 159138663 5399435 0.03392912129719225 0.6046471680446134 chr8 146364022 6878992 0.04699920039092667 0.6688926781293848 chr9 141213431 4729201 0.033489739371887366 0.4857445555804316 chr10 135534747 4317126 0.031852540367379 0.5935669880722009 chr11 135006516 5423994 0.0401757941816675 0.5042472890261803 chr12 133851895 4059156 0.03032572680424136 0.4583805159961793 chr13 115169878 3385918 0.029399336517487672 0.4985082430852082 chr14 107349540 3047737 0.028390778386195227 0.4356657927558363 chr15 102531392 1918784 0.018714112454456876 0.34460294658599827 chr16 90354753 2578193 0.028534115963993616 0.41715838114520437 chr17 81195210 2513463 0.030955803919960303 0.4413573987349535 chr18 78077248 2416608 0.030951500749616584 1.3103421996583644 chr19 59128983 1530717 0.025887761336940294 0.47231345489981147 chr20 63025520 1880444 0.02983623141863804 0.4563758964026562 chr21 48129895 1303243 0.027077619845212626 0.4480634135421975 chr22 51304566 966595 0.01884033089764369 0.3738117229401135 chrMT 16571 23959 1.4458391165288758 3.1533131722763446 chrX 155270560 5416756 0.03488591784559803 0.4880566584746759 chrY 59373566 415789 0.007002931237109794 0.3146495596244504