BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084966.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 = 2,562,052 number of mapped reads = 2,282,084 (89.07%) number of supplementary alignments = 18,946 (0.74%) number of secondary alignments = 0 number of mapped bases = 150,282,901 bp number of sequenced bases = 150,224,316 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,891 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.39 >>>>>>> ACTG content number of A's = 41,532,243 bp (27.65%) number of C's = 28,516,534 bp (18.98%) number of T's = 46,118,906 bp (30.7%) number of G's = 34,036,674 bp (22.66%) number of N's = 19,959 bp (0.01%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,298,188 number of insertions = 12,457 mapped reads with insertion percentage = 0.54% number of deletions = 36,401 mapped reads with deletion percentage = 1.58% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.0485X std coverageData = 0.4445X There is a 4.2% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 12181532 0.048872624473822276 0.8094276151505921 chr2 243199373 13149894 0.05407042722926757 0.5863013486559233 chr3 198022430 9286317 0.04689527847931166 0.2515779566010016 chr4 191154276 9270178 0.048495791953929404 0.26172520872514077 chr5 180915260 8844291 0.04888637365360998 0.25014699273700813 chr6 171115067 8314621 0.048590817546183704 0.3139153907441115 chr7 159138663 8366447 0.05257331463190689 0.43317962312627334 chr8 146364022 7620332 0.05206424294626175 0.544178800347338 chr9 141213431 6306176 0.04465705531933432 0.44401805129594 chr10 135534747 7470996 0.055122366517569105 0.5467984214521427 chr11 135006516 6944996 0.05144193188423587 0.41725546349386616 chr12 133851895 6625298 0.049497229755320234 0.25495761660006944 chr13 115169878 4479243 0.038892487148419135 0.21930712194883695 chr14 107349540 4612646 0.042968474760115415 0.2663490474259911 chr15 102531392 4330418 0.042235045438571636 0.23535078748702593 chr16 90354753 4539785 0.05024400874628034 0.30179588741028923 chr17 81195210 4276142 0.05266495400406009 0.31393972118578506 chr18 78077248 4145733 0.05309783715737522 0.8263610863942592 chr19 59128983 3134521 0.053011583168951174 0.5922899639813473 chr20 63025520 3043943 0.048296991440927424 0.2587465060466046 chr21 48129895 2020728 0.04198488278439003 0.2536010077764114 chr22 51304566 1692811 0.03299532833003597 0.20198784333106704 chrMT 16571 12845 0.7751493573109649 1.0764990601324784 chrX 155270560 9220606 0.05938412278541405 0.33456039445829855 chrY 59373566 392402 0.006609035408114109 0.13903262826151072