BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472578.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 9,934,822 number of mapped reads = 9,057,969 (91.17%) number of supplementary alignments = 275,026 (2.77%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,569,012 number of mapped paired reads (second in pair) = 4,488,957 number of mapped paired reads (both in pair) = 8,847,090 number of mapped paired reads (singletons) = 210,879 number of mapped bases = 735,298,214 bp number of sequenced bases = 734,989,216 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,486,247 duplication rate = 14.05% >>>>>>> Insert size mean insert size = 215,029.6848 std insert size = 4,453,188.5311 median insert size = 126 >>>>>>> Mapping quality mean mapping quality = 50.4552 >>>>>>> ACTG content number of A's = 189,247,135 bp (25.75%) number of C's = 147,293,370 bp (20.04%) number of T's = 218,390,955 bp (29.71%) number of G's = 179,562,062 bp (24.43%) number of N's = 495,694 bp (0.07%) GC percentage = 44.47% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 8,743,030 number of insertions = 68,976 mapped reads with insertion percentage = 0.75% number of deletions = 165,757 mapped reads with deletion percentage = 1.79% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.2375X std coverageData = 2.4449X There is a 12.6% of reference with a coverageData >= 1X There is a 5.94% of reference with a coverageData >= 2X There is a 2.18% of reference with a coverageData >= 3X There is a 1.09% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% 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 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 48112482 0.19302853411947968 2.961537733270963 chr2 243199373 72255432 0.29710369360203903 3.3754860763125625 chr3 198022430 38186940 0.19284148770419593 0.6776180404106976 chr4 191154276 36955949 0.19333048558118573 1.157530376737111 chr5 180915260 34203315 0.18905710330902986 0.7225331161698593 chr6 171115067 48083226 0.280999369856776 1.297524836820596 chr7 159138663 62718623 0.39411304467224284 4.557624606836103 chr8 146364022 36435742 0.2489391962732481 2.0106330738608023 chr9 141213431 25195017 0.17841799339894235 2.535713629611274 chr10 135534747 28549455 0.21064306852618392 2.103225947904601 chr11 135006516 28032398 0.20763737062883691 1.818721007614617 chr12 133851895 38112327 0.28473505735574384 0.8683331420196012 chr13 115169878 34101541 0.2960977435436721 0.8891552832721771 chr14 107349540 19168678 0.17856320576688078 6.179944380417615 chr15 102531392 16200570 0.1580059500216285 0.6219311430835404 chr16 90354753 27098372 0.29991086357128327 1.2380634582572303 chr17 81195210 28540299 0.3515022499479957 2.0316648183633412 chr18 78077248 16995477 0.21767515422674732 4.2993539764609405 chr19 59128983 15635940 0.2644378307673582 2.10140755387488 chr20 63025520 26048140 0.413295122356785 1.5238281475823496 chr21 48129895 11117205 0.2309833628350945 0.9716339194477444 chr22 51304566 8310918 0.1619917806146143 0.6520001339975883 chrMT 16571 19192 1.1581678836521634 2.3259053973065664 chrX 155270560 33593466 0.216354381667716 1.0929806871141559 chrY 59373566 1627510 0.027411356764389053 0.8443156371054412