BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081690.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 = 2,145,270 number of mapped reads = 1,921,742 (89.58%) number of supplementary alignments = 20,723 (0.97%) number of secondary alignments = 0 number of mapped bases = 130,024,271 bp number of sequenced bases = 129,976,302 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,038 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5352 >>>>>>> ACTG content number of A's = 36,488,073 bp (28.07%) number of C's = 23,482,059 bp (18.07%) number of T's = 41,754,751 bp (32.12%) number of G's = 28,157,062 bp (21.66%) number of N's = 94,357 bp (0.07%) GC percentage = 39.73% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,117,503 number of insertions = 10,759 mapped reads with insertion percentage = 0.56% number of deletions = 29,668 mapped reads with deletion percentage = 1.53% homopolymer indels = 49.74% >>>>>>> Coverage mean coverageData = 0.042X std coverageData = 0.3158X There is a 3.44% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.11% 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% 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 10227916 0.04103466606809377 0.4096531236113209 chr2 243199373 11228817 0.0461712415681269 0.3342536416097296 chr3 198022430 8941202 0.045152470858982996 0.25044109565716943 chr4 191154276 8432452 0.04411333178861246 0.25337384705440735 chr5 180915260 8375452 0.046294889662707284 0.2543236520104783 chr6 171115067 8068919 0.047154929963005535 0.29839765860924655 chr7 159138663 7301854 0.045883595239203434 0.4307658955543493 chr8 146364022 6958194 0.04754033064218473 0.5249431249739848 chr9 141213431 5601041 0.03966365635574707 0.29427715678574773 chr10 135534747 5736035 0.042321508889524836 0.2951984784191216 chr11 135006516 5763890 0.04269342081237027 0.29278922449016925 chr12 133851895 5903752 0.044106600059715256 0.24892826302565313 chr13 115169878 4427776 0.0384456081476443 0.23152782063256203 chr14 107349540 3914066 0.03646094803946062 0.23215538882193634 chr15 102531392 3648009 0.03557943502805463 0.22332480214644526 chr16 90354753 3295979 0.0364782027570813 0.23718245494292833 chr17 81195210 3072025 0.03783505209235865 0.24276396330254166 chr18 78077248 3662927 0.0469141407238124 0.5148398154689637 chr19 59128983 2047683 0.03463078335035798 0.3214603040096938 chr20 63025520 2582978 0.040983049406018386 0.24280919685665214 chr21 48129895 1693556 0.03518719498556978 0.2306794913093611 chr22 51304566 1346786 0.02625080192667452 0.19095666443926132 chrMT 16571 16879 1.018586687586748 1.2794668152074495 chrX 155270560 7501095 0.04830983413726337 0.2733806688338138 chrY 59373566 274988 0.004631488699870242 0.0991224171001559