BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081895.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,046,096 number of mapped reads = 1,799,547 (87.95%) number of supplementary alignments = 12,729 (0.62%) number of secondary alignments = 0 number of mapped bases = 123,827,381 bp number of sequenced bases = 123,780,631 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,113 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1641 >>>>>>> ACTG content number of A's = 35,891,778 bp (29%) number of C's = 23,215,224 bp (18.76%) number of T's = 38,596,796 bp (31.18%) number of G's = 26,075,464 bp (21.07%) number of N's = 1,369 bp (0%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,050,119 number of insertions = 9,692 mapped reads with insertion percentage = 0.53% number of deletions = 26,084 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.3528X There is a 3.49% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 9542547 0.03828494774342007 0.5818176960423804 chr2 243199373 10603056 0.043598204506884154 0.3973112376193191 chr3 198022430 8559324 0.043224012552517406 0.23270412422592976 chr4 191154276 8576150 0.044865070138425785 0.25218492601785897 chr5 180915260 7799624 0.04311202935562208 0.23119072736806684 chr6 171115067 7282552 0.0425593849079345 0.2565364455498558 chr7 159138663 6868321 0.043159348397944 0.4282442788909096 chr8 146364022 6411858 0.043807610042309444 0.6320037256156215 chr9 141213431 5162371 0.03655722379551843 0.3167246926539196 chr10 135534747 5672569 0.04185324520508383 0.3645845124444208 chr11 135006516 5597450 0.04146059142804633 0.29573514468073975 chr12 133851895 5720009 0.042733866412574886 0.23043372326355435 chr13 115169878 4135536 0.03590813910560885 0.20966215903323396 chr14 107349540 3750996 0.03494189169324806 0.22367079653935612 chr15 102531392 3369232 0.03286049213103437 0.20232730943137078 chr16 90354753 3228018 0.03572604531385305 0.23780371733955386 chr17 81195210 2886140 0.035545692904790815 0.2284962090661198 chr18 78077248 3418027 0.043777503530862155 0.5713040712127413 chr19 59128983 2121941 0.03588664800813503 0.4308206726465245 chr20 63025520 2348572 0.0372638258280138 0.2250108724345185 chr21 48129895 1640557 0.03408602906779663 0.2209026639532022 chr22 51304566 1136478 0.02215159562990943 0.16266114163363724 chrMT 16571 1133 0.06837245790839418 0.28261368856437313 chrX 155270560 7673922 0.049422904122970894 0.27046778713889047 chrY 59373566 320998 0.005406412678665789 0.14075477554701218