BamQC report ----------------------------------- >>>>>>> Input bam file = B7_input_d_s.bam outfile = QUALIMAP_B7_input/genome_results.txt >>>>>>> Reference number of bases = 2,725,537,669 bp number of contigs = 22 >>>>>>> Globals number of windows = 421 number of reads = 37,299,406 number of mapped reads = 36,270,327 (97.24%) number of mapped bases = 1,303,765,232 bp number of sequenced bases = 1,303,537,890 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 171,590 duplication rate = 0.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.5825 >>>>>>> ACTG content number of A's = 348,628,926 bp (26.74%) number of C's = 302,732,437 bp (23.22%) number of T's = 349,683,835 bp (26.83%) number of G's = 302,492,692 bp (23.21%) number of N's = 108,283 bp (0.01%) GC percentage = 46.43% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 4,163,567 number of insertions = 73,561 mapped reads with insertion percentage = 0.19% number of deletions = 75,675 mapped reads with deletion percentage = 0.2% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 1.116X std coverageData = 1.3014X There is a 63.7% of reference with a coverageData >= 1X There is a 30.28% of reference with a coverageData >= 2X There is a 11.64% of reference with a coverageData >= 3X There is a 3.84% of reference with a coverageData >= 4X There is a 1.15% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.11% 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 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 1 87833224 95037407 1.0820211609219763 1.1707366943433313 2 91729544 93358336 1.017756460230523 1.2334322922407364 3 63799692 66314949 1.0394242812332073 1.085086307275645 4 70909143 76949418 1.0851833028076507 1.1324915182347735 5 74314364 82289800 1.1073202483439137 1.1376136054258505 6 70481271 75829971 1.0758882455454017 1.115769905528639 7 72394548 82031120 1.1331118470412993 1.1305775671067653 8 62305007 102337730 1.6425281839708323 1.4270258875078943 9 65205555 75835235 1.1630180128058107 2.3746487481153817 10 64472795 69547736 1.078714456229174 1.1145934535525532 11 63004071 76885240 1.2203217788894942 1.3911994558843386 12 45140598 49479245 1.0961140789495079 1.132985888908557 13 44652192 49390921 1.1061253387067762 1.1629458084709718 14 48751186 51870426 1.0639828536684215 1.3593290817880836 15 40767811 66298920 1.6262565581458372 1.3961936688511145 16 38505094 41833009 1.08642791522597 1.1223947370335257 17 41899931 48272493 1.1520900356613952 1.3056623411063037 18 33695330 36565486 1.0851796376530516 1.112767441885869 19 29501366 34525921 1.1703160118077245 1.1592240691143312 X 51516852 26473012 0.5138709174232928 0.7871070915972131 Y 7391595 2532948 0.3426794893389045 0.7137932953444426 MT 15365 105909 6.892873413602343 4.363512054545273