BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053600.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,957,655 number of mapped reads = 4,987,559 (62.68%) number of supplementary alignments = 197 (0%) number of secondary alignments = 0 number of mapped bases = 232,312,344 bp number of sequenced bases = 232,265,291 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,338,948 duplication rate = 19.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3592 >>>>>>> ACTG content number of A's = 70,744,661 bp (30.46%) number of C's = 44,912,596 bp (19.34%) number of T's = 68,738,173 bp (29.59%) number of G's = 47,769,040 bp (20.57%) number of N's = 100,821 bp (0.04%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 2,271,613 number of insertions = 13,218 mapped reads with insertion percentage = 0.26% number of deletions = 33,413 mapped reads with deletion percentage = 0.67% homopolymer indels = 45.52% >>>>>>> Coverage mean coverageData = 0.075X std coverageData = 0.92X There is a 3.26% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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% 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 18258763 0.07325463393730121 0.7346208020059534 chr2 243199373 20525098 0.08439617975495356 2.403561674666185 chr3 198022430 16624122 0.0839507019482591 0.6503803278430168 chr4 191154276 16149269 0.08448290740825488 0.6671274844435873 chr5 180915260 14411186 0.07965710576321754 0.6365679653412859 chr6 171115067 13670890 0.07989296465635022 0.7182400132266382 chr7 159138663 12534158 0.07876249406468873 0.718894084602873 chr8 146364022 11955241 0.08168155559431128 0.6765336678459019 chr9 141213431 9350640 0.06621636436267879 0.6054452828008949 chr10 135534747 10720024 0.07909428568896801 0.6801314517659061 chr11 135006516 10476991 0.07760359507388517 0.6976478032510386 chr12 133851895 11033831 0.08243313253054804 0.6400960089000735 chr13 115169878 7778659 0.06754074185960325 0.5884576465933997 chr14 107349540 7150758 0.06661191095928311 0.6273347852794008 chr15 102531392 6893018 0.06722836650847382 0.5697575641574855 chr16 90354753 6360149 0.07039086255927234 0.6078087353305425 chr17 81195210 5731890 0.07059394267223398 0.5861436313095175 chr18 78077248 6149443 0.0787610111462945 0.7433953610121915 chr19 59128983 3773689 0.06382130739505532 0.6660530600497273 chr20 63025520 4801965 0.07619080334442302 0.6220660597527498 chr21 48129895 3115569 0.06473251188268747 0.589609394505167 chr22 51304566 2256987 0.043991932413968766 0.4286163560516487 chrMT 16571 52531 3.17005612214109 5.625865301108794 chrX 155270560 11962814 0.07704495945657695 0.6505489865194634 chrY 59373566 574659 0.009678701124335365 0.20153791494571235