BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240206.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,654,599 number of mapped reads = 1,376,881 (83.22%) number of supplementary alignments = 5,741 (0.35%) number of secondary alignments = 0 number of mapped bases = 85,796,499 bp number of sequenced bases = 85,748,626 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,850 duplication rate = 4.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2235 >>>>>>> ACTG content number of A's = 23,253,224 bp (27.12%) number of C's = 14,979,650 bp (17.47%) number of T's = 27,761,811 bp (32.38%) number of G's = 19,733,110 bp (23.01%) number of N's = 20,831 bp (0.02%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 768,568 number of insertions = 5,912 mapped reads with insertion percentage = 0.43% number of deletions = 27,608 mapped reads with deletion percentage = 1.98% homopolymer indels = 49.35% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.268X There is a 2.31% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 6076930 0.024380801843619078 0.3544977770935761 chr2 243199373 9291106 0.03820365934907242 0.3335462824129537 chr3 198022430 5614668 0.028353697103908886 0.19597293550088135 chr4 191154276 5386978 0.028181310471966634 0.2029551343794588 chr5 180915260 5019566 0.027745398591583707 0.1959015333565359 chr6 171115067 4809780 0.028108454061500032 0.23493458350684318 chr7 159138663 4718686 0.029651411612022907 0.4600508568691116 chr8 146364022 5278839 0.03606650683594907 0.35713296808428274 chr9 141213431 2946104 0.02086277473139223 0.23640547313037813 chr10 135534747 4222294 0.031152852633428384 0.24803506211720583 chr11 135006516 4409331 0.03266013471527552 0.290678855411043 chr12 133851895 4499573 0.03361605750893553 0.2158252162487095 chr13 115169878 1838167 0.01596048404253758 0.1493741495558266 chr14 107349540 3245476 0.03023278907389822 0.21218766729309724 chr15 102531392 2040137 0.019897681677822146 0.17815840557224602 chr16 90354753 2373981 0.026274002431283278 0.19357686472034874 chr17 81195210 2037186 0.025089977598432223 0.20566558303235252 chr18 78077248 2111804 0.027047623399841143 0.37596177385271656 chr19 59128983 1413727 0.023909205406086556 0.26927353781281466 chr20 63025520 1719647 0.027284931564229856 0.19530375579028125 chr21 48129895 1433377 0.029781427946186045 0.2068996979506544 chr22 51304566 805500 0.015700356962380306 0.14318812167221828 chrMT 16571 22413 1.352543600265524 1.6486946987086775 chrX 155270560 4300882 0.02769927538098658 0.21341973225011968 chrY 59373566 180347 0.003037496518231699 0.07143122283670836