BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548918.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 5,389,125 number of mapped reads = 4,666,376 (86.59%) number of secondary alignments = 0 number of mapped bases = 184,643,144 bp number of sequenced bases = 184,622,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,328 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6314 >>>>>>> ACTG content number of A's = 53,685,536 bp (29.08%) number of C's = 37,972,079 bp (20.57%) number of T's = 54,546,422 bp (29.54%) number of G's = 38,416,115 bp (20.81%) number of N's = 1,865 bp (0%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 520,528 number of insertions = 6,298 mapped reads with insertion percentage = 0.13% number of deletions = 16,019 mapped reads with deletion percentage = 0.34% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0596X std coverageData = 0.3912X There is a 4.86% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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% 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 14220069 0.05705128814904738 0.4189587104067108 chr2 243199373 15454971 0.06354856432956346 0.4063149823837854 chr3 198022430 12466237 0.06295366136048325 0.30559548240083456 chr4 191154276 12418402 0.06496533721275478 0.3153669732002245 chr5 180915260 11692541 0.06462993226773683 0.3091648172108935 chr6 171115067 10930131 0.06387591222460849 0.33024344553994606 chr7 159138663 10315126 0.06481847846113926 0.588995727294719 chr8 146364022 9709906 0.06634079787722696 0.6336248122227245 chr9 141213431 7814684 0.05533952361797654 0.4142390930771243 chr10 135534747 8388760 0.06189379613480225 0.36233184501927584 chr11 135006516 8219698 0.06088371319796149 0.41759317954949365 chr12 133851895 8324408 0.06219118526487802 0.307075788899936 chr13 115169878 6075263 0.05275045094690471 0.27841890408072634 chr14 107349540 5750753 0.05357035530846243 0.3407456405722444 chr15 102531392 5331481 0.05199852353511401 0.2759213071320186 chr16 90354753 5149519 0.05699223149887865 0.3179553711743594 chr17 81195210 4594883 0.05659056734997052 0.30627019177016435 chr18 78077248 4737501 0.06067710019697416 0.6248529104194797 chr19 59128983 3293786 0.0557051015066503 0.4489446605421459 chr20 63025520 3795641 0.06022387439246832 0.30764436593573996 chr21 48129895 2360162 0.049037339474769265 0.3029667095781534 chr22 51304566 1898994 0.03701413242634194 0.2625197923041659 chrMT 16571 7996 0.4825297205962223 0.9437636931214438 chrX 155270560 11129081 0.07167540968487522 0.36319699038968306 chrY 59373566 563151 0.009484877495820278 0.1414067498724235