BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472592.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 = 7,738,870 number of mapped reads = 7,111,888 (91.9%) number of supplementary alignments = 204,130 (2.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,585,186 number of mapped paired reads (second in pair) = 3,526,702 number of mapped paired reads (both in pair) = 6,946,998 number of mapped paired reads (singletons) = 164,890 number of mapped bases = 577,502,831 bp number of sequenced bases = 577,251,597 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,065,054 duplication rate = 13.07% >>>>>>> Insert size mean insert size = 216,237.9504 std insert size = 4,463,025.4161 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 50.3172 >>>>>>> ACTG content number of A's = 149,790,841 bp (25.95%) number of C's = 114,437,827 bp (19.82%) number of T's = 172,798,004 bp (29.93%) number of G's = 139,867,256 bp (24.23%) number of N's = 357,669 bp (0.06%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 6,768,865 number of insertions = 55,644 mapped reads with insertion percentage = 0.77% number of deletions = 134,455 mapped reads with deletion percentage = 1.85% homopolymer indels = 42.63% >>>>>>> Coverage mean coverageData = 0.1866X std coverageData = 1.8319X There is a 10.68% of reference with a coverageData >= 1X There is a 4.62% of reference with a coverageData >= 2X There is a 1.48% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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% 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 35533326 0.1425606317747148 2.388316846201542 chr2 243199373 54458370 0.22392479605611484 2.8971150252134303 chr3 198022430 29028500 0.146591979504544 0.5578733407222607 chr4 191154276 27504704 0.14388746396653979 0.9213212498243041 chr5 180915260 26289676 0.14531486177561803 0.5862373281040489 chr6 171115067 36310606 0.2121999344452818 1.0653798735578894 chr7 159138663 49488272 0.310975793481437 3.0763773560528618 chr8 146364022 27583091 0.1884554047032132 1.6016085337470045 chr9 141213431 17977657 0.12730840737096744 2.0192078408908802 chr10 135534747 30047050 0.22169259665936442 1.7630895588883488 chr11 135006516 28492419 0.2110447691280323 1.65865694957128 chr12 133851895 28532795 0.21316691108482252 0.7058992106493568 chr13 115169878 25024348 0.2172820570323084 0.7069725346921422 chr14 107349540 13980174 0.1302304043408104 3.7995681684059566 chr15 102531392 15961533 0.15567459573746936 0.5921951399641684 chr16 90354753 19355123 0.21421256057221472 0.9995123117985738 chr17 81195210 17267221 0.212663049950853 1.3924196224108323 chr18 78077248 12081257 0.1547346673899162 3.061548062253288 chr19 59128983 9051135 0.15307442375594385 1.6397758519299084 chr20 63025520 21559057 0.34206868900089993 1.1713856576536152 chr21 48129895 8261626 0.1716526911184826 0.7701398611458724 chr22 51304566 5094060 0.09929057776261084 0.4700568225577238 chrMT 16571 126610 7.640456218695311 5.680495033353808 chrX 155270560 37058977 0.23867355794942713 1.058609669578337 chrY 59373566 1435244 0.024173114345195302 0.7676377498836982