BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472553.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,068,346 number of mapped reads = 13,791,295 (98.03%) number of supplementary alignments = 61,787 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,923,406 number of mapped paired reads (second in pair) = 6,867,889 number of mapped paired reads (both in pair) = 13,671,240 number of mapped paired reads (singletons) = 120,055 number of mapped bases = 1,353,160,274 bp number of sequenced bases = 1,352,995,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,435,510 duplication rate = 46.46% >>>>>>> Insert size mean insert size = 39,146.0817 std insert size = 1,954,388.1787 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 54.9268 >>>>>>> ACTG content number of A's = 372,946,342 bp (27.56%) number of C's = 305,713,415 bp (22.6%) number of T's = 369,721,692 bp (27.33%) number of G's = 304,407,787 bp (22.5%) number of N's = 205,975 bp (0.02%) GC percentage = 45.09% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 8,431,176 number of insertions = 75,494 mapped reads with insertion percentage = 0.54% number of deletions = 67,068 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.59% >>>>>>> Coverage mean coverageData = 0.4371X std coverageData = 15.4006X There is a 4.05% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 155793684 0.6250483283650475 20.526951179770354 chr2 243199373 90445802 0.3718998157121071 11.870247194780804 chr3 198022430 150753294 0.7612940311862652 18.157353190011506 chr4 191154276 48748402 0.2550212478636889 10.255804818194761 chr5 180915260 72169868 0.3989153153802504 12.868924161477983 chr6 171115067 85368517 0.4988953836543219 15.889515273191567 chr7 159138663 65783070 0.4133695027964386 17.236783663242075 chr8 146364022 66281850 0.452856167070894 15.198195478524074 chr9 141213431 82797352 0.5863277410206116 14.5257351848304 chr10 135534747 33231635 0.24518904366272953 8.239596741409429 chr11 135006516 59177931 0.43833388752880637 14.139914721465606 chr12 133851895 72426777 0.5410963886615128 14.184405246262363 chr13 115169878 23507333 0.20411007989432792 7.125748367903868 chr14 107349540 26582447 0.24762515982835137 11.139533173926212 chr15 102531392 34273260 0.3342708933474735 10.82379632583546 chr16 90354753 30518155 0.33775926541462625 9.090509605363764 chr17 81195210 51467686 0.6338758899693714 14.524525689907103 chr18 78077248 22095804 0.2829992675971366 10.400811169878407 chr19 59128983 27058830 0.4576238018502703 13.491512687562341 chr20 63025520 47949290 0.7607916602671426 34.2933676968689 chr21 48129895 4069922 0.0845612067094682 3.0165384499368524 chr22 51304566 15102312 0.2943658465018494 11.207500711138533 chrMT 16571 3144 0.1897290447166737 0.6973691841351793 chrX 155270560 85260031 0.5491062246442596 26.130592119005154 chrY 59373566 2293878 0.03863466782507219 2.1510845476862457