BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819138.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,666,266 number of mapped reads = 1,519,885 (91.22%) number of supplementary alignments = 6,993 (0.42%) number of secondary alignments = 0 number of mapped bases = 88,624,823 bp number of sequenced bases = 88,596,165 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,950 duplication rate = 4.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7797 >>>>>>> ACTG content number of A's = 23,203,013 bp (26.19%) number of C's = 16,746,638 bp (18.9%) number of T's = 26,934,304 bp (30.4%) number of G's = 21,710,901 bp (24.51%) number of N's = 1,309 bp (0%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 464,544 number of insertions = 6,818 mapped reads with insertion percentage = 0.45% number of deletions = 16,920 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.43% >>>>>>> Coverage mean coverageData = 0.0286X std coverageData = 0.2815X There is a 2.43% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 8662482 0.03475410398275397 0.5088702527359076 chr2 243199373 6871487 0.028254542416110588 0.34740849689998565 chr3 198022430 4681121 0.023639347320402036 0.17620337549437018 chr4 191154276 4651359 0.024333010473697174 0.22904799782774857 chr5 180915260 4783760 0.026441992787120335 0.18620274563811176 chr6 171115067 3747174 0.02189856256199812 0.1997565713370193 chr7 159138663 4465999 0.028063569944658893 0.32690634522731504 chr8 146364022 7971697 0.054464867055921705 0.31773344028472533 chr9 141213431 4331591 0.030674072355058066 0.23681732544630354 chr10 135534747 4594696 0.033900502282267146 0.31662477799640815 chr11 135006516 3009378 0.022290612995301648 0.22361882091764154 chr12 133851895 4121187 0.030789156926018867 0.2016623949831391 chr13 115169878 1978403 0.01717812881593918 0.15157784698099142 chr14 107349540 2065373 0.019239700514785626 0.16278727618561964 chr15 102531392 2371841 0.023132827456395014 0.17500938762679186 chr16 90354753 2787372 0.030849201701652597 0.21198333807108702 chr17 81195210 3273058 0.0403109740094274 0.24221769206701194 chr18 78077248 2028395 0.025979335234766473 0.3962612363891527 chr19 59128983 1895152 0.032051151632355994 0.3579214942756946 chr20 63025520 2584369 0.04100511983082408 0.23929743985696308 chr21 48129895 1238117 0.025724489945386335 0.21693826762509036 chr22 51304566 778364 0.015171437177735798 0.14289373708468678 chrMT 16571 123043 7.425200651740993 4.9928268734089025 chrX 155270560 5259012 0.03386998797453941 0.22829300292835142 chrY 59373566 350393 0.005901498319976267 0.21466743903525018