BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717093.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 = 2,077,778 number of mapped reads = 1,910,207 (91.94%) number of supplementary alignments = 11,067 (0.53%) number of secondary alignments = 0 number of mapped bases = 112,247,422 bp number of sequenced bases = 112,216,569 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,786 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9561 >>>>>>> ACTG content number of A's = 28,080,964 bp (25.02%) number of C's = 20,878,845 bp (18.61%) number of T's = 34,254,015 bp (30.52%) number of G's = 29,001,878 bp (25.84%) number of N's = 867 bp (0%) GC percentage = 44.45% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 553,676 number of insertions = 7,786 mapped reads with insertion percentage = 0.41% number of deletions = 19,437 mapped reads with deletion percentage = 1.01% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.3097X There is a 3.08% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% 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% 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 13288212 0.05331265353196452 0.48840423441409486 chr2 243199373 11557892 0.047524349497397755 0.4260620649248391 chr3 198022430 7088628 0.03579709631883621 0.21602318766486744 chr4 191154276 4557365 0.023841292464731472 0.20624932388833817 chr5 180915260 8101618 0.04478128600097084 0.24344357037643155 chr6 171115067 4126502 0.02411536326020899 0.19413771124343646 chr7 159138663 7479526 0.04700005554275644 0.4986489602822625 chr8 146364022 4917993 0.033601105878328485 0.3000328804500393 chr9 141213431 3060753 0.021674659260987716 0.22547485011933935 chr10 135534747 5030448 0.03711555974646118 0.2805764478094099 chr11 135006516 4796889 0.03553079615801655 0.2987704897857563 chr12 133851895 4774152 0.035667421817225674 0.21832379361208037 chr13 115169878 3216899 0.027931773966105963 0.19127394505039796 chr14 107349540 2377771 0.022149801480285804 0.17894033089069586 chr15 102531392 4947185 0.048250442167019444 0.25235997517104436 chr16 90354753 3340679 0.036972919399159886 0.23301068781045145 chr17 81195210 4294611 0.052892418161120586 0.28756481159569036 chr18 78077248 3563893 0.04564573023885268 0.508458465526147 chr19 59128983 1780979 0.030120237312385365 0.3627721217287601 chr20 63025520 2805599 0.0445152852368374 0.24595479008042925 chr21 48129895 1372831 0.028523457198483395 0.2109207782137989 chr22 51304566 1326303 0.025851558709218982 0.18312379612318191 chrMT 16571 2989 0.1803753545350311 0.47697199304029525 chrX 155270560 4175861 0.026894093767678817 0.21344020026630375 chrY 59373566 261844 0.004410110721663577 0.12287119727035058