BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013217.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 = 2,211,196 number of mapped reads = 1,827,637 (82.65%) number of supplementary alignments = 13,003 (0.59%) number of secondary alignments = 0 number of mapped bases = 117,791,941 bp number of sequenced bases = 117,738,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,794 duplication rate = 4.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0435 >>>>>>> ACTG content number of A's = 31,822,231 bp (27.03%) number of C's = 20,965,152 bp (17.81%) number of T's = 38,282,125 bp (32.51%) number of G's = 26,667,554 bp (22.65%) number of N's = 1,502 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 896,155 number of insertions = 7,941 mapped reads with insertion percentage = 0.43% number of deletions = 31,077 mapped reads with deletion percentage = 1.68% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.3376X There is a 2.98% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13044519 0.052334950852539704 0.5921145770488078 chr2 243199373 12405070 0.051007820649274456 0.41887833728552704 chr3 198022430 7470407 0.037725054681936786 0.24150054107105406 chr4 191154276 6329447 0.03311172071295962 0.23705160262627498 chr5 180915260 4948840 0.02735446418394999 0.203570084424698 chr6 171115067 6273519 0.03666257513138805 0.2888166629595054 chr7 159138663 3926815 0.024675430382370373 0.3013326167908237 chr8 146364022 5756386 0.03932924171761282 0.380921171201688 chr9 141213431 3467483 0.024554909369775176 0.25970796940841945 chr10 135534747 9848056 0.072660747284237 0.4997402267916707 chr11 135006516 6587646 0.048795022604686725 0.3269343948351194 chr12 133851895 7008768 0.052362112617083234 0.28515967875957543 chr13 115169878 1328828 0.011537982179680698 0.1304884760799303 chr14 107349540 3796773 0.03536832109387707 0.23753801954330725 chr15 102531392 1723639 0.0168108416981211 0.16034286640554807 chr16 90354753 3673069 0.04065164120364537 0.26629985238939546 chr17 81195210 3313169 0.040804980983484125 0.2862182021807292 chr18 78077248 2891604 0.03703516804280806 0.4601023983932092 chr19 59128983 1707829 0.02888311134997874 0.45409248621879955 chr20 63025520 2055090 0.03260726765919583 0.22710236287459692 chr21 48129895 2898013 0.06021232749416969 0.31345877109892023 chr22 51304566 1184417 0.023085995893620852 0.18369160201649803 chrMT 16571 45989 2.775270050087502 2.279241274238966 chrX 155270560 5859619 0.037738119834178484 0.2629526218898204 chrY 59373566 246946 0.004159190977345036 0.10476130575881334