BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618596.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 42,047,662 number of mapped reads = 40,444,066 (96.19%) number of supplementary alignments = 49,761 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,419,705 number of mapped paired reads (second in pair) = 20,024,361 number of mapped paired reads (both in pair) = 39,708,710 number of mapped paired reads (singletons) = 735,356 number of mapped bases = 3,872,454,540 bp number of sequenced bases = 3,869,997,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,083,674 duplication rate = 13.45% >>>>>>> Insert size mean insert size = 25,842.1169 std insert size = 1,607,722.3189 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 53.8672 >>>>>>> ACTG content number of A's = 1,038,569,565 bp (26.84%) number of C's = 879,436,905 bp (22.72%) number of T's = 1,042,245,692 bp (26.93%) number of G's = 909,571,420 bp (23.5%) number of N's = 173,538 bp (0%) GC percentage = 46.23% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 49,995,891 number of insertions = 687,701 mapped reads with insertion percentage = 1.67% number of deletions = 1,787,312 mapped reads with deletion percentage = 4.32% homopolymer indels = 52.3% >>>>>>> Coverage mean coverageData = 1.2509X std coverageData = 5.2568X There is a 24.53% of reference with a coverageData >= 1X There is a 16.26% of reference with a coverageData >= 2X There is a 11.84% of reference with a coverageData >= 3X There is a 9.14% of reference with a coverageData >= 4X There is a 7.31% of reference with a coverageData >= 5X There is a 6% of reference with a coverageData >= 6X There is a 5.02% of reference with a coverageData >= 7X There is a 4.26% of reference with a coverageData >= 8X There is a 3.66% of reference with a coverageData >= 9X There is a 3.17% of reference with a coverageData >= 10X There is a 2.77% of reference with a coverageData >= 11X There is a 2.45% of reference with a coverageData >= 12X There is a 2.17% of reference with a coverageData >= 13X There is a 1.93% of reference with a coverageData >= 14X There is a 1.73% of reference with a coverageData >= 15X There is a 1.56% of reference with a coverageData >= 16X There is a 1.41% of reference with a coverageData >= 17X There is a 1.28% of reference with a coverageData >= 18X There is a 1.17% of reference with a coverageData >= 19X There is a 1.06% of reference with a coverageData >= 20X There is a 0.97% of reference with a coverageData >= 21X There is a 0.89% of reference with a coverageData >= 22X There is a 0.82% of reference with a coverageData >= 23X There is a 0.76% of reference with a coverageData >= 24X There is a 0.7% of reference with a coverageData >= 25X There is a 0.65% of reference with a coverageData >= 26X There is a 0.6% of reference with a coverageData >= 27X There is a 0.56% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.48% of reference with a coverageData >= 30X There is a 0.45% of reference with a coverageData >= 31X There is a 0.42% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.37% of reference with a coverageData >= 34X There is a 0.35% of reference with a coverageData >= 35X There is a 0.32% of reference with a coverageData >= 36X There is a 0.31% of reference with a coverageData >= 37X There is a 0.29% of reference with a coverageData >= 38X There is a 0.27% of reference with a coverageData >= 39X There is a 0.25% of reference with a coverageData >= 40X There is a 0.24% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 351454222 1.410043515999906 6.21127885431743 chr2 243199373 314555707 1.29340673505766 5.483900996436089 chr3 198022430 233370188 1.1785038088867004 4.282124661793725 chr4 191154276 173526745 0.907783747406205 4.460524154118063 chr5 180915260 210832307 1.1653649725291277 4.165228253213558 chr6 171115067 197176811 1.1523053723843033 4.3812707857186 chr7 159138663 191182394 1.2013572968122774 4.403880633468977 chr8 146364022 186512656 1.2743067145285198 4.648994721753411 chr9 141213431 169160889 1.1979093475888989 5.754370558111399 chr10 135534747 205487265 1.5161223933225034 5.511018471585598 chr11 135006516 207476493 1.5367887354414804 5.821877280355543 chr12 133851895 178316452 1.3321922113990243 4.826563882990407 chr13 115169878 94184183 0.8177848638512928 3.4368801662351642 chr14 107349540 120803768 1.1253310261040708 4.612766916891421 chr15 102531392 128251549 1.2508515343281401 4.857340291858316 chr16 90354753 145401826 1.6092327317855653 8.797434498201492 chr17 81195210 136005009 1.6750373451832934 6.084694741710642 chr18 78077248 95079193 1.2177579952613085 5.673922677612381 chr19 59128983 95140643 1.6090356737574871 6.354578539144962 chr20 63025520 120640559 1.9141541235994561 6.247956487515723 chr21 48129895 49572471 1.0299725565576239 8.3926901710931 chr22 51304566 77745357 1.5153691583708164 6.1126665094976795 chrMT 16571 249 0.015026250678896867 0.13836691231929507 chrX 155270560 185160530 1.1925024937116218 4.097289347473395 chrY 59373566 5417074 0.09123713404716166 2.778571809727535