BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212691.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,747,022 number of mapped reads = 2,564,213 (93.35%) number of supplementary alignments = 28,254 (1.03%) number of secondary alignments = 0 number of mapped bases = 181,093,024 bp number of sequenced bases = 181,023,679 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,108 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3957 >>>>>>> ACTG content number of A's = 54,375,601 bp (30.04%) number of C's = 33,595,197 bp (18.56%) number of T's = 57,446,982 bp (31.73%) number of G's = 35,579,621 bp (19.65%) number of N's = 26,278 bp (0.01%) GC percentage = 38.21% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,485,078 number of insertions = 14,670 mapped reads with insertion percentage = 0.57% number of deletions = 42,164 mapped reads with deletion percentage = 1.63% homopolymer indels = 47.83% >>>>>>> Coverage mean coverageData = 0.0585X std coverageData = 0.6825X There is a 4.78% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13222872 0.05305050774577609 1.3052830643509459 chr2 243199373 10520222 0.043257603299824296 0.47510405894696434 chr3 198022430 11036126 0.05573169665678782 0.2799595987999392 chr4 191154276 21255423 0.11119512178738811 0.39011802052654276 chr5 180915260 8713666 0.04816435053626764 0.25568736450981855 chr6 171115067 19098802 0.11161379494419389 0.6051270943119225 chr7 159138663 14260065 0.08960779694372574 0.6865525716973462 chr8 146364022 12738438 0.08703257689926013 1.8222891313087257 chr9 141213431 5675916 0.04019388212442767 0.46516913663314896 chr10 135534747 4609309 0.03400831965252423 0.4357659904023065 chr11 135006516 5520958 0.040894011367569844 0.45866271086510596 chr12 133851895 1403919 0.010488600105362723 0.14249410322459105 chr13 115169878 7820393 0.06790311091585945 0.299689999646117 chr14 107349540 10107160 0.09415187060885404 0.38056469576152574 chr15 102531392 6513595 0.06352781204804085 0.289189846888281 chr16 90354753 2592119 0.028688241779599576 0.2836103163948399 chr17 81195210 3355977 0.04133220420268634 0.27934213453039697 chr18 78077248 7340159 0.09401149743392595 1.0011923927644573 chr19 59128983 1670063 0.028244405962470215 0.816206140070198 chr20 63025520 2252770 0.03574377490261088 0.2449198467237558 chr21 48129895 2747815 0.05709164750930788 0.3011682451671988 chr22 51304566 1398739 0.027263440840723612 0.1882596359997019 chrMT 16571 60928 3.6767847444330455 2.8280523364412766 chrX 155270560 6762779 0.04355480523803096 0.2943446201130608 chrY 59373566 414811 0.0069864592603381785 0.2171009005895716