BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472650.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 = 5,628,486 number of mapped reads = 5,555,390 (98.7%) number of supplementary alignments = 11,834 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,797,920 number of mapped paired reads (second in pair) = 2,757,470 number of mapped paired reads (both in pair) = 5,512,212 number of mapped paired reads (singletons) = 43,178 number of mapped bases = 544,016,701 bp number of sequenced bases = 543,931,657 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,154,480 duplication rate = 49.88% >>>>>>> Insert size mean insert size = 24,643.3403 std insert size = 1,557,654.3495 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 53.8229 >>>>>>> ACTG content number of A's = 150,392,560 bp (27.65%) number of C's = 120,738,805 bp (22.2%) number of T's = 154,684,514 bp (28.44%) number of G's = 118,016,756 bp (21.7%) number of N's = 99,022 bp (0.02%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 2,879,396 number of insertions = 26,283 mapped reads with insertion percentage = 0.46% number of deletions = 33,700 mapped reads with deletion percentage = 0.59% homopolymer indels = 44.63% >>>>>>> Coverage mean coverageData = 0.1757X std coverageData = 6.0158X There is a 1.5% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 74060690 0.2971334221871407 8.134689547935823 chr2 243199373 43537142 0.1790183151500148 5.941905171199431 chr3 198022430 30357515 0.15330341618371213 5.40718728538526 chr4 191154276 16593047 0.08680447723806084 3.7052458827812393 chr5 180915260 25417730 0.14049522411763385 4.985451081324155 chr6 171115067 47079414 0.27513307171249857 7.479587307696974 chr7 159138663 41800536 0.26266738209306184 7.48947156055335 chr8 146364022 39566354 0.2703284144514695 7.607517506494 chr9 141213431 15927337 0.11278910856574259 4.162765312330547 chr10 135534747 13293675 0.09808315058868262 3.8269431098179982 chr11 135006516 15566119 0.1152990200858157 4.374436726603632 chr12 133851895 19801527 0.1479360975800903 4.611493125370233 chr13 115169878 20264982 0.17595731064332637 6.734374036049375 chr14 107349540 15581887 0.14515094335755888 5.209992270680129 chr15 102531392 8198869 0.07996447566029338 3.291951322160906 chr16 90354753 34907785 0.3863414357405194 11.672914393854919 chr17 81195210 28016270 0.3450483101158307 8.100253260472368 chr18 78077248 7375008 0.09445783744836908 3.7900169541280437 chr19 59128983 11540073 0.1951677910644937 4.609192603501663 chr20 63025520 9954009 0.15793616617522552 5.820034890241861 chr21 48129895 6010294 0.12487652424755966 8.04348197733297 chr22 51304566 9624783 0.1876009047615762 6.070813163436931 chrMT 16571 30304 1.8287369500935369 1.9728698219816594 chrX 155270560 8590505 0.0553260386257382 2.1952747954624576 chrY 59373566 920846 0.015509359838686463 0.7501077893542191