BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013184.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,809,757 number of mapped reads = 1,356,440 (74.95%) number of supplementary alignments = 6,006 (0.33%) number of secondary alignments = 0 number of mapped bases = 80,590,547 bp number of sequenced bases = 80,558,298 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,561 duplication rate = 10.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6485 >>>>>>> ACTG content number of A's = 22,781,821 bp (28.28%) number of C's = 13,019,519 bp (16.16%) number of T's = 25,595,107 bp (31.77%) number of G's = 19,134,891 bp (23.75%) number of N's = 26,960 bp (0.03%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 828,713 number of insertions = 5,037 mapped reads with insertion percentage = 0.37% number of deletions = 19,752 mapped reads with deletion percentage = 1.44% homopolymer indels = 50.56% >>>>>>> Coverage mean coverageData = 0.026X std coverageData = 0.2561X There is a 1.88% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 5096196 0.020446071426237288 0.2582480299314007 chr2 243199373 9678221 0.039795419209407254 0.30313178772201776 chr3 198022430 6672124 0.033693779033011566 0.2581430977811639 chr4 191154276 7435494 0.03889786906990247 0.2947713380574541 chr5 180915260 3963840 0.021909926227339806 0.20821977821804044 chr6 171115067 3980395 0.023261510922354955 0.22352306617049447 chr7 159138663 4852098 0.030489749684525124 0.3827808628074151 chr8 146364022 5453497 0.037259819219780665 0.34707879474169145 chr9 141213431 2305722 0.01632792280218728 0.19460672563546463 chr10 135534747 2396830 0.01768424742033126 0.19426258012190362 chr11 135006516 3757226 0.027829960444279593 0.24047509664853492 chr12 133851895 2483410 0.018553416819388324 0.18854693957231614 chr13 115169878 2017000 0.017513259847336125 0.18448584610108973 chr14 107349540 2271285 0.02115784566938992 0.20502221269122298 chr15 102531392 2630251 0.025653128751046313 0.23349533044666163 chr16 90354753 1464789 0.016211532336323248 0.20010046035573303 chr17 81195210 2427629 0.029898672594109922 0.24950825050393308 chr18 78077248 1316074 0.016856050049305016 0.24543399715802522 chr19 59128983 1302017 0.022019945785301264 0.22587608878936224 chr20 63025520 1679902 0.026654313998519964 0.2357410590195455 chr21 48129895 1085591 0.02255544085437959 0.21151499653532027 chr22 51304566 589889 0.011497787545849233 0.15174140161011176 chrMT 16571 197041 11.890712690845453 12.080668203243924 chrX 155270560 5381745 0.03466043401917273 0.2705870900966984 chrY 59373566 152281 0.0025647945754176194 0.06501496006458572