BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472760.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 = 18,673,064 number of mapped reads = 18,497,757 (99.06%) number of supplementary alignments = 61,846 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,281,603 number of mapped paired reads (second in pair) = 9,216,154 number of mapped paired reads (both in pair) = 18,392,458 number of mapped paired reads (singletons) = 105,299 number of mapped bases = 1,820,533,182 bp number of sequenced bases = 1,820,291,579 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,930,843 duplication rate = 48.14% >>>>>>> Insert size mean insert size = 23,761.1118 std insert size = 1,510,278.4643 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 55.1571 >>>>>>> ACTG content number of A's = 507,350,775 bp (27.87%) number of C's = 404,873,319 bp (22.24%) number of T's = 504,454,905 bp (27.71%) number of G's = 403,259,879 bp (22.15%) number of N's = 352,701 bp (0.02%) GC percentage = 44.4% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 11,121,459 number of insertions = 98,851 mapped reads with insertion percentage = 0.53% number of deletions = 103,252 mapped reads with deletion percentage = 0.55% homopolymer indels = 46.77% >>>>>>> Coverage mean coverageData = 0.5881X std coverageData = 19.2814X There is a 4.96% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 205320091 0.8237495665055936 25.83537217736068 chr2 243199373 135940805 0.558968566913205 20.43481778732736 chr3 198022430 218687497 1.1043572033733755 25.24775791133888 chr4 191154276 86297186 0.45145307657151235 17.65945236447163 chr5 180915260 81646450 0.45129664573347766 13.488970976940855 chr6 171115067 127577570 0.7455659646850386 21.160624847406137 chr7 159138663 74459182 0.4678886990523478 14.546274719145607 chr8 146364022 76988291 0.526005571232526 15.456724578726192 chr9 141213431 107779850 0.7632407855029031 19.85225673729514 chr10 135534747 45878785 0.3385020152802587 15.210544918120554 chr11 135006516 88900734 0.658492172333371 25.22295543828789 chr12 133851895 87470631 0.6534881781090959 18.340588659172518 chr13 115169878 50157779 0.435511262762647 23.086172776411477 chr14 107349540 45442315 0.42331168815441594 15.53355159775667 chr15 102531392 44617927 0.43516357409836004 15.662750289241142 chr16 90354753 49470770 0.5475170741709625 15.009413800962488 chr17 81195210 80616907 0.992877621721774 23.27327238230584 chr18 78077248 33190332 0.4250960792060704 21.049138601146176 chr19 59128983 30027143 0.5078244454162183 10.05663767891801 chr20 63025520 45368541 0.7198439774872147 28.393251566587356 chr21 48129895 8940487 0.1857574590594889 6.873570692947028 chr22 51304566 11835570 0.23069233253040286 6.593993673917444 chrMT 16571 4334 0.26154124675638163 0.6543838105020541 chrX 155270560 81778139 0.5266815486464401 13.45331539283929 chrY 59373566 2135866 0.035973348813173864 1.3156397450981934