BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082895.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,042,096 number of mapped reads = 3,637,399 (89.99%) number of supplementary alignments = 26,616 (0.66%) number of secondary alignments = 0 number of mapped bases = 253,432,484 bp number of sequenced bases = 253,335,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,092 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7647 >>>>>>> ACTG content number of A's = 74,112,131 bp (29.25%) number of C's = 46,672,305 bp (18.42%) number of T's = 81,732,973 bp (32.26%) number of G's = 50,803,963 bp (20.05%) number of N's = 14,588 bp (0.01%) GC percentage = 38.48% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,221,661 number of insertions = 20,425 mapped reads with insertion percentage = 0.56% number of deletions = 55,834 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.83% >>>>>>> Coverage mean coverageData = 0.0819X std coverageData = 0.6281X There is a 6.12% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% 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% 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 26257645 0.10534635739182371 1.3339069618061095 chr2 243199373 25948984 0.10669840008181271 0.6584380692409921 chr3 198022430 18718050 0.09452489801281602 0.3873323843887079 chr4 191154276 15321661 0.08015337831103501 0.36898935589847137 chr5 180915260 13773806 0.07613401987206607 0.3496631059777728 chr6 171115067 17039231 0.09957761931040239 0.5582781136801718 chr7 159138663 12813837 0.08051994881972836 0.5469117044813372 chr8 146364022 23095326 0.15779373704283695 0.9087545165818022 chr9 141213431 7326770 0.05188437068709137 0.5026918293094406 chr10 135534747 8449962 0.062345355615707906 0.48218920454734204 chr11 135006516 10231752 0.07578709756497976 0.48383692523862704 chr12 133851895 7648538 0.0571417984033771 0.3106541825275706 chr13 115169878 6215676 0.05396963258049123 0.2898625780298078 chr14 107349540 5268911 0.049081821869008474 0.32034247691258766 chr15 102531392 4680233 0.045646829802135136 0.2654630300126757 chr16 90354753 9249941 0.10237359621800969 0.464036165288759 chr17 81195210 5754479 0.07087214873882339 0.42390808072830544 chr18 78077248 8689252 0.11129044917156916 1.1445878477671605 chr19 59128983 3700779 0.06258824035583362 0.8128385443908807 chr20 63025520 4722528 0.07493040914220145 0.3570865354673352 chr21 48129895 5014306 0.10418277455207413 0.42560220758961465 chr22 51304566 2782282 0.0542306897206771 0.2855534241698864 chrMT 16571 387674 23.394725725665317 15.004367152405703 chrX 155270560 9928340 0.06394219226104421 0.36233574438951094 chrY 59373566 412521 0.006947889907774783 0.13422041428295173