BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432727.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 465,734,722 number of mapped reads = 465,480,773 (99.95%) number of supplementary alignments = 849,728 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 232,744,411 number of mapped paired reads (second in pair) = 232,736,362 number of mapped paired reads (both in pair) = 465,379,750 number of mapped paired reads (singletons) = 101,023 number of mapped bases = 69,551,730,900 bp number of sequenced bases = 69,531,228,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,204,497 duplication rate = 9.4% >>>>>>> Insert size mean insert size = 21,326.2416 std insert size = 1,470,830.8145 median insert size = 330 >>>>>>> Mapping quality mean mapping quality = 57.4857 >>>>>>> ACTG content number of A's = 20,467,999,071 bp (29.44%) number of C's = 14,311,563,916 bp (20.58%) number of T's = 20,446,393,683 bp (29.41%) number of G's = 14,288,696,186 bp (20.55%) number of N's = 16,575,285 bp (0.02%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 368,504,624 number of insertions = 6,846,740 mapped reads with insertion percentage = 1.43% number of deletions = 7,255,657 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.69% >>>>>>> Coverage mean coverageData = 22.4673X std coverageData = 25.3866X There is a 87.4% of reference with a coverageData >= 1X There is a 86.93% of reference with a coverageData >= 2X There is a 86.61% of reference with a coverageData >= 3X There is a 86.36% of reference with a coverageData >= 4X There is a 86.11% of reference with a coverageData >= 5X There is a 85.86% of reference with a coverageData >= 6X There is a 85.58% of reference with a coverageData >= 7X There is a 85.25% of reference with a coverageData >= 8X There is a 84.84% of reference with a coverageData >= 9X There is a 84.35% of reference with a coverageData >= 10X There is a 83.75% of reference with a coverageData >= 11X There is a 83.05% of reference with a coverageData >= 12X There is a 82.25% of reference with a coverageData >= 13X There is a 81.33% of reference with a coverageData >= 14X There is a 80.28% of reference with a coverageData >= 15X There is a 79.05% of reference with a coverageData >= 16X There is a 77.6% of reference with a coverageData >= 17X There is a 75.87% of reference with a coverageData >= 18X There is a 73.77% of reference with a coverageData >= 19X There is a 71.24% of reference with a coverageData >= 20X There is a 68.24% of reference with a coverageData >= 21X There is a 64.76% of reference with a coverageData >= 22X There is a 60.79% of reference with a coverageData >= 23X There is a 56.38% of reference with a coverageData >= 24X There is a 51.63% of reference with a coverageData >= 25X There is a 46.63% of reference with a coverageData >= 26X There is a 41.51% of reference with a coverageData >= 27X There is a 36.4% of reference with a coverageData >= 28X There is a 31.43% of reference with a coverageData >= 29X There is a 26.71% of reference with a coverageData >= 30X There is a 22.35% of reference with a coverageData >= 31X There is a 18.39% of reference with a coverageData >= 32X There is a 14.9% of reference with a coverageData >= 33X There is a 11.88% of reference with a coverageData >= 34X There is a 9.32% of reference with a coverageData >= 35X There is a 7.2% of reference with a coverageData >= 36X There is a 5.48% of reference with a coverageData >= 37X There is a 4.11% of reference with a coverageData >= 38X There is a 3.04% of reference with a coverageData >= 39X There is a 2.23% of reference with a coverageData >= 40X There is a 1.61% of reference with a coverageData >= 41X There is a 1.16% of reference with a coverageData >= 42X There is a 0.83% of reference with a coverageData >= 43X There is a 0.59% of reference with a coverageData >= 44X There is a 0.43% of reference with a coverageData >= 45X There is a 0.32% of reference with a coverageData >= 46X There is a 0.24% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5740761551 23.03208524804438 56.23239906252755 chr2 243199373 6037392914 24.82487039142161 32.89173968554004 chr3 198022430 4986876760 25.18339341659427 8.854406796348265 chr4 191154276 4590538195 24.014833939681267 10.63029464840965 chr5 180915260 4441420919 24.54973073581521 9.771734763572246 chr6 171115067 4147291074 24.23685503977274 38.53384630725431 chr7 159138663 3776525374 23.731036209597914 14.27666186108219 chr8 146364022 3642259981 24.88494051495797 23.464245498331966 chr9 141213431 2827570993 20.023385686309116 13.629885019917056 chr10 135534747 3336951401 24.620634006126856 21.578437466594185 chr11 135006516 3366411614 24.935178787963093 11.296442435665288 chr12 133851895 3354696693 25.06275083367329 10.510418857653661 chr13 115169878 2371539251 20.591662439722302 13.941909338975607 chr14 107349540 2253793181 20.994903014954698 15.00298710435658 chr15 102531392 2011600948 19.619366408289864 13.592800384900668 chr16 90354753 1990834731 22.03353630992716 24.07715634836072 chr17 81195210 1980676783 24.39401022548005 21.447380180299604 chr18 78077248 1908316247 24.44138716313362 22.433385882938058 chr19 59128983 1444507173 24.42976523036089 16.423930272645183 chr20 63025520 1618539905 25.680706878737375 12.118621035544562 chr21 48129895 868837753 18.051935351199084 17.089682224802228 chr22 51304566 890983571 17.36655507425986 15.489714423764974 chrMT 16571 13722545 828.106028604188 775.929820484465 chrX 155270560 1791371219 11.537095113201111 7.962988635506309 chrY 59373566 158310124 2.66634016895667 33.92316778182539