BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617658.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,199,824 (94.37%) number of supplementary alignments = 171,676 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,299,281 number of mapped paired reads (second in pair) = 14,900,543 number of mapped paired reads (both in pair) = 29,439,552 number of mapped paired reads (singletons) = 760,272 number of mapped bases = 2,919,079,382 bp number of sequenced bases = 2,917,295,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,970,407 duplication rate = 10.78% >>>>>>> Insert size mean insert size = 45,481.1539 std insert size = 2,004,612.5787 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 52.5555 >>>>>>> ACTG content number of A's = 868,054,362 bp (29.76%) number of C's = 580,792,037 bp (19.91%) number of T's = 867,841,260 bp (29.75%) number of G's = 597,337,784 bp (20.48%) number of N's = 3,270,268 bp (0.11%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0141 number of mismatches = 40,334,490 number of insertions = 459,227 mapped reads with insertion percentage = 1.49% number of deletions = 1,074,070 mapped reads with deletion percentage = 3.48% homopolymer indels = 47.6% >>>>>>> Coverage mean coverageData = 0.9429X std coverageData = 10.5235X There is a 33.24% of reference with a coverageData >= 1X There is a 19.19% of reference with a coverageData >= 2X There is a 11.71% of reference with a coverageData >= 3X There is a 7.46% of reference with a coverageData >= 4X There is a 4.9% of reference with a coverageData >= 5X There is a 3.32% of reference with a coverageData >= 6X There is a 2.3% of reference with a coverageData >= 7X There is a 1.63% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.65% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179489882 0.7201180935071773 10.1575312979379 chr2 243199373 301736056 1.2406942184016239 12.12228311622547 chr3 198022430 244391617 1.234161286678484 2.4691702341107087 chr4 191154276 163135432 0.8534228760857016 8.426574089962067 chr5 180915260 192844512 1.0659383404141807 2.312882307054036 chr6 171115067 141404934 0.8263733666422256 5.667659960522449 chr7 159138663 227933265 1.4322934521575061 13.129080756900787 chr8 146364022 129655104 0.8858399914700349 4.0614717510233636 chr9 141213431 119723211 0.8478174501687449 20.392399940002214 chr10 135534747 123713728 0.9127823730692469 21.348927021292862 chr11 135006516 160697058 1.1902911263927438 11.849163952675715 chr12 133851895 124671055 0.9314104592990633 2.248735122017492 chr13 115169878 125446798 1.0892327071840782 2.311962910813385 chr14 107349540 83532900 0.7781393380912485 2.4371382939128203 chr15 102531392 62498760 0.6095573148953249 1.7007453347392998 chr16 90354753 80899567 0.8953548575358288 16.547593883448766 chr17 81195210 72092277 0.8878883003073703 12.593294678030835 chr18 78077248 54120748 0.6931692571951307 18.168515527260837 chr19 59128983 30942775 0.5233097785564822 6.0041187024348845 chr20 63025520 78872091 1.2514310234965138 3.068326547833119 chr21 48129895 42378877 0.8805104810637963 4.325240569894459 chr22 51304566 18910331 0.36858963001460726 1.283614709951862 chrMT 16571 3135509 189.2166435338845 134.45315009032552 chrX 155270560 145075432 0.9343395940608445 4.349281730549412 chrY 59373566 11777463 0.19836206233595605 17.162158202599752