BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236085.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 = 2,361,519 number of mapped reads = 2,076,325 (87.92%) number of supplementary alignments = 10,999 (0.47%) number of secondary alignments = 0 number of mapped bases = 135,958,522 bp number of sequenced bases = 135,884,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,122 duplication rate = 4.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7545 >>>>>>> ACTG content number of A's = 37,081,789 bp (27.29%) number of C's = 24,146,393 bp (17.77%) number of T's = 43,890,693 bp (32.3%) number of G's = 30,694,031 bp (22.59%) number of N's = 71,203 bp (0.05%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,104,326 number of insertions = 9,605 mapped reads with insertion percentage = 0.46% number of deletions = 42,804 mapped reads with deletion percentage = 2.04% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.0439X std coverageData = 0.3626X There is a 3.68% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% 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 12432422 0.0498792017051785 0.5897310535007247 chr2 243199373 9987056 0.04106530323990597 0.42978679511640333 chr3 198022430 8363055 0.04223286725650221 0.23514244021198108 chr4 191154276 6240594 0.03264689721092088 0.22474210753417503 chr5 180915260 7654496 0.04230984163524956 0.2375296363249834 chr6 171115067 15110693 0.08830720324587198 0.45811460509003826 chr7 159138663 7185067 0.045149725808617605 0.43954938312631825 chr8 146364022 9203390 0.06288013867233028 0.5876157044743104 chr9 141213431 6143006 0.04350157032867504 0.3401369075595338 chr10 135534747 4380040 0.032316731295481 0.28361520613870667 chr11 135006516 5426594 0.040195052511391376 0.27308881047435146 chr12 133851895 4688397 0.0350267510220905 0.22027480394721272 chr13 115169878 5088163 0.0441796334975713 0.2425280523273826 chr14 107349540 4692745 0.04371462607105722 0.24726996942347967 chr15 102531392 3699661 0.03608320269366869 0.22720377172256648 chr16 90354753 3792582 0.04197434970576479 0.25032612896826023 chr17 81195210 3859284 0.047530931935516885 0.2691384981763909 chr18 78077248 3375748 0.04323600135086728 0.5512249711135985 chr19 59128983 2007196 0.033946059921240314 0.4086039216340469 chr20 63025520 3158223 0.05011022519131932 0.2606226978749931 chr21 48129895 2028117 0.042138404831342346 0.2494480426298497 chr22 51304566 1540385 0.03002432571011321 0.19683765839283487 chrMT 16571 63867 3.8541427795546435 3.1339112995140193 chrX 155270560 5564431 0.03583699962182142 0.23777406681965782 chrY 59373566 273310 0.004603226964673134 0.11494697011195511