BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716557.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 16,419,281 number of mapped reads = 16,012,643 (97.52%) number of supplementary alignments = 8,654 (0.05%) number of secondary alignments = 0 number of mapped bases = 1,090,226,352 bp number of sequenced bases = 1,090,049,494 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 779,336 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9597 >>>>>>> ACTG content number of A's = 306,247,107 bp (28.09%) number of C's = 236,497,832 bp (21.7%) number of T's = 323,246,440 bp (29.65%) number of G's = 224,003,559 bp (20.55%) number of N's = 54,556 bp (0.01%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 3,257,860 number of insertions = 87,662 mapped reads with insertion percentage = 0.54% number of deletions = 90,476 mapped reads with deletion percentage = 0.56% homopolymer indels = 37.41% >>>>>>> Coverage mean coverageData = 0.3522X std coverageData = 3.575X There is a 27.01% of reference with a coverageData >= 1X There is a 5.31% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% 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 0.02% 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 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 89545658 0.35925951815381835 7.455145418804097 chr2 243199373 102625798 0.4219821652254013 2.4236626122470284 chr3 198022430 75873117 0.38315415581962103 1.365768557510585 chr4 191154276 62301399 0.3259220787715991 1.7341688254326248 chr5 180915260 57387328 0.3172055690603435 0.687116098220954 chr6 171115067 59137026 0.3455980062819366 1.330625875388872 chr7 159138663 58666670 0.36865126861094716 5.156650912276757 chr8 146364022 77974142 0.5327411814359679 2.0962450333155345 chr9 141213431 44588071 0.3157495054418726 1.4620995871260958 chr10 135534747 57647346 0.42533259755153413 8.818268149507546 chr11 135006516 38464774 0.2849105001717102 1.300239131612556 chr12 133851895 49118653 0.3669627015740046 1.3396939618964585 chr13 115169878 29052258 0.2522556983172284 0.5394566911818987 chr14 107349540 32266584 0.3005749628736183 0.7626253136565136 chr15 102531392 26419442 0.2576717382321309 0.5480137831695303 chr16 90354753 39043345 0.4321116897967725 4.320645907569734 chr17 81195210 42754789 0.5265678726614538 1.2075663123146803 chr18 78077248 25397869 0.32529154972265417 2.9888832651645325 chr19 59128983 23280341 0.3937213159915164 6.24672035146165 chr20 63025520 24282898 0.38528675368326987 1.254382050341449 chr21 48129895 11983313 0.24897858181489904 1.6625729592932958 chr22 51304566 16945684 0.3302958259114793 0.7233448686754717 chrMT 16571 4137195 249.66477581316758 66.59674105907345 chrX 155270560 38257707 0.24639382378732969 1.0829822159757438 chrY 59373566 3074945 0.05178979817382032 2.1047751105571306