BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549074.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,039,987 number of mapped reads = 8,828,549 (87.93%) number of secondary alignments = 0 number of mapped bases = 350,861,077 bp number of sequenced bases = 350,827,274 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 329,676 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2471 >>>>>>> ACTG content number of A's = 101,915,774 bp (29.05%) number of C's = 74,084,488 bp (21.12%) number of T's = 103,126,157 bp (29.4%) number of G's = 71,616,950 bp (20.41%) number of N's = 83,905 bp (0.02%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,359,646 number of insertions = 7,580 mapped reads with insertion percentage = 0.09% number of deletions = 26,512 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.16% >>>>>>> Coverage mean coverageData = 0.1133X std coverageData = 0.852X There is a 9.24% of reference with a coverageData >= 1X There is a 1.55% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 29303807 0.11756763887862089 1.9882745117781777 chr2 243199373 30227487 0.12429097422056265 0.5867507912936434 chr3 198022430 24257633 0.12249942089893553 0.41121840673537924 chr4 191154276 23052611 0.12059688897568789 0.4354938365782974 chr5 180915260 22073961 0.12201270915455115 0.4177850042319334 chr6 171115067 20719839 0.12108716878800627 0.5069548130715297 chr7 159138663 19449123 0.12221494533983863 0.8493539046768912 chr8 146364022 18389909 0.12564500994650174 1.6058045722355485 chr9 141213431 15032974 0.10645569542177613 0.5652498552750431 chr10 135534747 16986453 0.12532913792210051 0.6615600254732422 chr11 135006516 16384357 0.12135974977681818 0.5805736673183562 chr12 133851895 16152992 0.12067809723575448 0.42475848368619057 chr13 115169878 11486241 0.09973303088851063 0.36127056648414124 chr14 107349540 10944040 0.10194771211874779 0.42581480424087287 chr15 102531392 10457358 0.10199176853075398 0.36808356492254274 chr16 90354753 9952381 0.11014784136480346 0.4367887747293934 chr17 81195210 9363122 0.1153161867553517 0.45055711733401616 chr18 78077248 9500445 0.12168006997377777 1.0788125199266798 chr19 59128983 6687942 0.11310767851359797 1.4671845752418502 chr20 63025520 7634235 0.12112926636702086 0.4217239839393623 chr21 48129895 4524287 0.09400159713624973 0.41686977281728277 chr22 51304566 4151760 0.08092379146136817 0.3597108759617349 chrMT 16571 10756 0.6490857522177298 1.133817853816106 chrX 155270560 11098560 0.07147884312389934 0.3873941164284971 chrY 59373566 3018804 0.050844242705583825 0.5199529036040178