BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716974.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 = 976,814 number of mapped reads = 841,273 (86.12%) number of supplementary alignments = 3,438 (0.35%) number of secondary alignments = 0 number of mapped bases = 47,491,055 bp number of sequenced bases = 47,476,346 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,457 duplication rate = 1.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8918 >>>>>>> ACTG content number of A's = 11,229,358 bp (23.65%) number of C's = 9,118,927 bp (19.21%) number of T's = 15,017,445 bp (31.63%) number of G's = 12,109,859 bp (25.51%) number of N's = 757 bp (0%) GC percentage = 44.71% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 253,281 number of insertions = 2,936 mapped reads with insertion percentage = 0.35% number of deletions = 9,123 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.5% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 0.1623X There is a 1.44% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 3948324 0.015840778988470403 0.18934433889078844 chr2 243199373 4661929 0.01916916537445185 0.22473289027802798 chr3 198022430 3345695 0.016895535520900333 0.14192121533457777 chr4 191154276 2859354 0.014958357510140134 0.13306162663105123 chr5 180915260 2541014 0.01404532707743946 0.1238868577976837 chr6 171115067 2628589 0.015361528625646974 0.1399592105670845 chr7 159138663 2346144 0.014742765559114947 0.2685735515172982 chr8 146364022 3409977 0.023297918118156114 0.17509889017927108 chr9 141213431 1964172 0.013909243519477974 0.136055398332854 chr10 135534747 2373258 0.017510328919564812 0.19945937267312663 chr11 135006516 1415231 0.010482686628251336 0.11807763707266575 chr12 133851895 2218772 0.016576321164522925 0.13748422852603642 chr13 115169878 1222138 0.010611611484037518 0.10737563400730263 chr14 107349540 1530880 0.014260703865149306 0.12635069681242564 chr15 102531392 1140271 0.011121189108600028 0.11087426798737234 chr16 90354753 1496264 0.01655988147076225 0.13958367236264602 chr17 81195210 2084845 0.02567694572130548 0.17308154704166046 chr18 78077248 1135663 0.014545376906727041 0.1770570716159226 chr19 59128983 1045684 0.017684795965457415 0.19613849595633145 chr20 63025520 1068179 0.01694835679261353 0.13814486389239847 chr21 48129895 494476 0.010273780983731629 0.1086333657892552 chr22 51304566 727759 0.014185072728224618 0.12566612180196252 chrMT 16571 43467 2.6230764588739364 2.2554816714744166 chrX 155270560 1673896 0.010780511128445728 0.1176545675746909 chrY 59373566 115074 0.0019381352300786516 0.06044597335516688