BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230397.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 = 129,893 number of mapped reads = 114,870 (88.43%) number of supplementary alignments = 934 (0.72%) number of secondary alignments = 0 number of mapped bases = 7,791,884 bp number of sequenced bases = 7,788,523 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,096 duplication rate = 1.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5201 >>>>>>> ACTG content number of A's = 2,283,556 bp (29.32%) number of C's = 1,428,503 bp (18.34%) number of T's = 2,478,332 bp (31.82%) number of G's = 1,593,871 bp (20.46%) number of N's = 4,261 bp (0.05%) GC percentage = 38.81% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 67,227 number of insertions = 681 mapped reads with insertion percentage = 0.59% number of deletions = 2,029 mapped reads with deletion percentage = 1.74% homopolymer indels = 49.04% >>>>>>> Coverage mean coverageData = 0.0025X std coverageData = 0.0544X There is a 0.24% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% 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 646091 0.0025921339630283207 0.06214439920542678 chr2 243199373 851829 0.0035025953788129214 0.06354035246404637 chr3 198022430 814892 0.004115149985786964 0.06602124181374501 chr4 191154276 522889 0.002735429261336534 0.054439587030409645 chr5 180915260 119954 6.630397015707796E-4 0.02752504997916781 chr6 171115067 664131 0.0038811953362353534 0.06534452977930322 chr7 159138663 469700 0.0029515140516167336 0.060193735375772404 chr8 146364022 480518 0.003283033585945049 0.06649919934589536 chr9 141213431 578750 0.004098406191971923 0.06727133580181859 chr10 135534747 370668 0.002734855881643399 0.05668313518456781 chr11 135006516 372157 0.002756585467326629 0.05621765433912573 chr12 133851895 316945 0.0023678783180469728 0.05023570030867133 chr13 115169878 175017 0.0015196421411508311 0.039985402574218114 chr14 107349540 77070 7.179350745238405E-4 0.02826072764114783 chr15 102531392 74319 7.248414222251074E-4 0.027925285803273785 chr16 90354753 356989 0.003950970902438304 0.06557551311968261 chr17 81195210 137281 0.001690752447096325 0.0423665255426479 chr18 78077248 163564 0.0020948996562993615 0.06034594858401277 chr19 59128983 65305 0.0011044499107992437 0.04208898074132795 chr20 63025520 162121 0.002572307217774641 0.05221228157403824 chr21 48129895 121962 0.002534017578887301 0.0521506296070782 chr22 51304566 46260 9.016741316942434E-4 0.030897232148790216 chrMT 16571 5364 0.3236980266731036 0.6302679611079703 chrX 155270560 184719 0.0011896588767374833 0.036085842662516084 chrY 59373566 13389 2.2550439365558742E-4 0.017103724623576417