BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004135.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 = 2,194,417 number of mapped reads = 1,961,340 (89.38%) number of supplementary alignments = 19,265 (0.88%) number of secondary alignments = 0 number of mapped bases = 130,787,999 bp number of sequenced bases = 130,734,188 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,298 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.225 >>>>>>> ACTG content number of A's = 36,957,429 bp (28.27%) number of C's = 24,127,455 bp (18.46%) number of T's = 41,412,816 bp (31.68%) number of G's = 28,227,323 bp (21.59%) number of N's = 9,165 bp (0.01%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,202,833 number of insertions = 10,484 mapped reads with insertion percentage = 0.53% number of deletions = 32,679 mapped reads with deletion percentage = 1.65% homopolymer indels = 45.92% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.398X There is a 3.56% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10106498 0.04054753388157055 0.5618884837635479 chr2 243199373 12814186 0.05269004538099693 0.5138827915582145 chr3 198022430 4667632 0.02357122877443732 0.17437329839389132 chr4 191154276 5362533 0.028053429471805277 0.21783227894614343 chr5 180915260 3526361 0.019491783059096286 0.16411537524754863 chr6 171115067 13359897 0.07807551511521776 0.5124460216997947 chr7 159138663 7488357 0.04705554802857682 0.5567468132381453 chr8 146364022 10095296 0.06897389031848278 0.5781280329168834 chr9 141213431 5665002 0.04011659485845932 0.42130927285728215 chr10 135534747 4240225 0.03128515081081016 0.29979390462070055 chr11 135006516 5590868 0.04141183822564535 0.348990909785715 chr12 133851895 4454111 0.03327641345682853 0.21541171439658108 chr13 115169878 4387640 0.03809711424718189 0.22233502129793165 chr14 107349540 4683990 0.043633070062526584 0.2552779643899194 chr15 102531392 7906588 0.07711382675854045 0.31757070437378365 chr16 90354753 3355921 0.03714161002686821 0.2748377111558927 chr17 81195210 1452441 0.017888259664578736 0.1755862794045862 chr18 78077248 4955219 0.06346559499638102 0.8411557396194554 chr19 59128983 2138506 0.03616679826879485 0.43558263493777655 chr20 63025520 3277651 0.052005140140057554 0.2688136663664502 chr21 48129895 1507245 0.031316191319345286 0.23423231582687573 chr22 51304566 1038108 0.020234222427688017 0.1588168680641831 chrMT 16571 66429 4.008750226298956 3.034912031769907 chrX 155270560 8229042 0.0529980828303833 0.3015947076523913 chrY 59373566 418253 0.007044431186767525 0.1638567112085133