BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472651.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 = 17,123,666 number of mapped reads = 16,991,248 (99.23%) number of supplementary alignments = 21,080 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,535,193 number of mapped paired reads (second in pair) = 8,456,055 number of mapped paired reads (both in pair) = 16,904,828 number of mapped paired reads (singletons) = 86,420 number of mapped bases = 1,676,818,711 bp number of sequenced bases = 1,676,590,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,726,117 duplication rate = 49.33% >>>>>>> Insert size mean insert size = 16,732.8724 std insert size = 1,328,757.6554 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 54.8041 >>>>>>> ACTG content number of A's = 455,722,761 bp (27.18%) number of C's = 382,139,972 bp (22.79%) number of T's = 464,681,243 bp (27.72%) number of G's = 373,671,695 bp (22.29%) number of N's = 375,315 bp (0.02%) GC percentage = 45.08% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 7,036,319 number of insertions = 74,287 mapped reads with insertion percentage = 0.43% number of deletions = 90,950 mapped reads with deletion percentage = 0.53% homopolymer indels = 44.15% >>>>>>> Coverage mean coverageData = 0.5417X std coverageData = 11.6881X There is a 3.66% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.6% of reference with a coverageData >= 5X There is a 0.57% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.5% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.45% of reference with a coverageData >= 13X There is a 0.43% of reference with a coverageData >= 14X There is a 0.43% of reference with a coverageData >= 15X There is a 0.42% of reference with a coverageData >= 16X There is a 0.41% of reference with a coverageData >= 17X There is a 0.4% of reference with a coverageData >= 18X There is a 0.39% of reference with a coverageData >= 19X There is a 0.39% of reference with a coverageData >= 20X There is a 0.38% of reference with a coverageData >= 21X There is a 0.37% of reference with a coverageData >= 22X There is a 0.37% of reference with a coverageData >= 23X There is a 0.36% of reference with a coverageData >= 24X There is a 0.35% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.33% of reference with a coverageData >= 30X There is a 0.32% of reference with a coverageData >= 31X There is a 0.32% of reference with a coverageData >= 32X There is a 0.31% of reference with a coverageData >= 33X There is a 0.31% of reference with a coverageData >= 34X There is a 0.31% of reference with a coverageData >= 35X There is a 0.3% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.29% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.28% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.27% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.26% of reference with a coverageData >= 47X There is a 0.26% of reference with a coverageData >= 48X There is a 0.25% of reference with a coverageData >= 49X There is a 0.25% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 193922089 0.7780204848516706 14.71132521821293 chr2 243199373 121260549 0.49860551655287366 11.687558696692129 chr3 198022430 142700311 0.72062700674868 12.41840363844414 chr4 191154276 60488717 0.3164392566347823 9.106252630256272 chr5 180915260 81155638 0.4485837070902698 10.536563622278583 chr6 171115067 119284018 0.6970982748117674 12.648568772753656 chr7 159138663 102507086 0.6441369059384393 14.122796602314187 chr8 146364022 94235514 0.6438434303206017 12.695462058250472 chr9 141213431 76711207 0.543228830691041 10.183144798433707 chr10 135534747 43141172 0.318303408940587 8.192171998177256 chr11 135006516 65311069 0.4837623467003622 11.103671947738345 chr12 133851895 75805340 0.566337443336159 10.22468150671199 chr13 115169878 43342577 0.376336050299541 10.855132186509318 chr14 107349540 46561388 0.43373626007153826 10.428666310235023 chr15 102531392 37092398 0.36176625788909605 8.625780905926193 chr16 90354753 90795982 1.0048832959567717 19.890257535326054 chr17 81195210 87238584 1.0744301788245882 17.450592696816162 chr18 78077248 25845267 0.33102174656565764 7.824737607296127 chr19 59128983 46496685 0.7863603032035914 11.162801295666018 chr20 63025520 33000560 0.5236063105865687 10.858095357562558 chr21 48129895 13431152 0.27906048828903535 12.505245929752418 chr22 51304566 28208863 0.5498314321575198 12.072782339148377 chrMT 16571 207861 12.543660611912378 6.813506079542602 chrX 155270560 44944183 0.28945720940273545 5.027798703493767 chrY 59373566 3130501 0.0527255007725155 1.7930786442856894