BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094118.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 490,440 number of mapped reads = 409,022 (83.4%) number of supplementary alignments = 1,716 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 205,086 number of mapped paired reads (second in pair) = 203,936 number of mapped paired reads (both in pair) = 406,278 number of mapped paired reads (singletons) = 2,744 number of mapped bases = 59,775,350 bp number of sequenced bases = 59,727,517 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 407,633 duplication rate = 46.92% >>>>>>> Insert size mean insert size = 5,666.8971 std insert size = 664,870.7175 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 11.1866 >>>>>>> ACTG content number of A's = 16,370,913 bp (27.41%) number of C's = 12,773,793 bp (21.39%) number of T's = 17,120,720 bp (28.66%) number of G's = 13,461,461 bp (22.54%) number of N's = 630 bp (0%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.0164 number of mismatches = 943,436 number of insertions = 21,772 mapped reads with insertion percentage = 5.24% number of deletions = 40,883 mapped reads with deletion percentage = 9.78% homopolymer indels = 67.81% >>>>>>> Coverage mean coverageData = 0.0193X std coverageData = 33.3636X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 14032 5.6296750410102287E-5 0.034413293185950246 chr2 243199373 242470 9.970009256561694E-4 0.9568564076065524 chr3 198022430 3216 1.6240584463083298E-5 0.0044769324700058895 chr4 191154276 8874 4.642323564867573E-5 0.02188304350409799 chr5 180915260 8725 4.8226998651191725E-5 0.013720882743974407 chr6 171115067 5232 3.057591649717204E-5 0.00976473807155946 chr7 159138663 79170 4.974906695049964E-4 0.7602874633207933 chr8 146364022 3568787 0.02438295252640707 9.882324393940817 chr9 141213431 4152 2.9402302391477195E-5 0.010982299045656457 chr10 135534747 4090 3.0176763453876517E-5 0.011318738461105437 chr11 135006516 3123 2.31322168183349E-5 0.008862495728713555 chr12 133851895 5518 4.12246685039461E-5 0.015971887128121306 chr13 115169878 2159 1.8746221125631477E-5 0.005610249458816067 chr14 107349540 3803 3.542632786316551E-5 0.024625966626308032 chr15 102531392 2726 2.6586979332144442E-5 0.013856371358466265 chr16 90354753 4273 4.7291369387064785E-5 0.015641471191178327 chr17 81195210 24868 3.0627422479725095E-4 0.08707781763741784 chr18 78077248 9887 1.2663100010902023E-4 0.07271874686236172 chr19 59128983 1091 1.8451188311491844E-5 0.004616167988562505 chr20 63025520 1294 2.0531365707097696E-5 0.004998945772569833 chr21 48129895 875 1.817996901925508E-5 0.005175071109899894 chr22 51304566 2947 5.744128115224676E-5 0.04524085113376507 chrMT 16571 55728874 3363.0362681793495 13991.937499698268 chrX 155270560 43986 2.8328615546952365E-4 0.15195532770351322 chrY 59373566 1178 1.9840479178899244E-5 0.012813290509716036