BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548975.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,697,809 number of mapped reads = 3,391,889 (44.06%) number of secondary alignments = 0 number of mapped bases = 133,811,120 bp number of sequenced bases = 133,792,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,052 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6306 >>>>>>> ACTG content number of A's = 41,700,124 bp (31.17%) number of C's = 25,021,632 bp (18.7%) number of T's = 41,783,607 bp (31.23%) number of G's = 25,280,132 bp (18.9%) number of N's = 6,526 bp (0%) GC percentage = 37.6% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 443,808 number of insertions = 6,261 mapped reads with insertion percentage = 0.18% number of deletions = 15,274 mapped reads with deletion percentage = 0.45% homopolymer indels = 45.05% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 0.3323X There is a 3.67% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 10485960 0.04206994533425856 0.5072761725324981 chr2 243199373 11617040 0.047767557361260135 0.3096781082998907 chr3 198022430 9482928 0.04788815085240596 0.25105493228108094 chr4 191154276 9425329 0.04930744525955569 0.26079689195700206 chr5 180915260 8686140 0.04801220195576647 0.25459271115475957 chr6 171115067 8385992 0.04900791115022034 0.2817825279104345 chr7 159138663 7692189 0.04833639327483856 0.45586717850349845 chr8 146364022 7009782 0.04789279430979288 0.5778484281937195 chr9 141213431 5705698 0.040404782743363836 0.280038859955497 chr10 135534747 6171018 0.045530892531935 0.28461202489301407 chr11 135006516 6172864 0.0457227116356369 0.3041025915883741 chr12 133851895 6203105 0.0463430495324702 0.25272507560354796 chr13 115169878 4657435 0.04043969726181355 0.23038276911899758 chr14 107349540 4256472 0.03965058443659843 0.2549005351909013 chr15 102531392 3874827 0.03779161605452504 0.22139515641337043 chr16 90354753 3337893 0.03694208538204957 0.22719240217081815 chr17 81195210 3157479 0.03888750333917481 0.23348590098195793 chr18 78077248 3667462 0.04697222422593583 0.4587600779591689 chr19 59128983 2215312 0.0374657551610519 0.50223669205215 chr20 63025520 2648324 0.04201986750763818 0.2394432197783475 chr21 48129895 1818473 0.037782608916973534 0.24009118979208532 chr22 51304566 1303774 0.02541243600033572 0.20129469237398281 chrMT 16571 5668 0.3420433287067769 0.6442205525002389 chrX 155270560 4643513 0.029905946111097943 0.22692872612821022 chrY 59373566 1186443 0.019982680508022713 0.23792873881678772