BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068061.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 = 1,924,422 number of mapped reads = 1,313,035 (68.23%) number of supplementary alignments = 13,715 (0.71%) number of secondary alignments = 0 number of mapped bases = 86,748,693 bp number of sequenced bases = 86,714,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 230,175 duplication rate = 12.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1595 >>>>>>> ACTG content number of A's = 24,323,559 bp (28.05%) number of C's = 15,355,185 bp (17.71%) number of T's = 28,238,550 bp (32.57%) number of G's = 18,713,877 bp (21.58%) number of N's = 83,153 bp (0.1%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 748,308 number of insertions = 6,755 mapped reads with insertion percentage = 0.51% number of deletions = 21,094 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.028X std coverageData = 0.4346X There is a 1.06% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 6621352 0.026565037123819243 0.6007894065167284 chr2 243199373 7149024 0.029395733680612737 0.4433552963209998 chr3 198022430 5930434 0.029948294241212977 0.3789111533204843 chr4 191154276 5946240 0.031107020593146448 0.42945440703403803 chr5 180915260 5665014 0.03131307994693206 0.3873957218536234 chr6 171115067 5259265 0.030735253722572544 0.4119632734853661 chr7 159138663 5146023 0.03233672385446647 0.49677969592550886 chr8 146364022 4434998 0.030301148734488862 0.4939185666008064 chr9 141213431 3936482 0.027876116118161594 0.41926501912602904 chr10 135534747 4162257 0.030709888734288926 0.5077407946591369 chr11 135006516 4389112 0.03251037157347279 0.4214713210969098 chr12 133851895 3641628 0.02720639853473871 0.36142721146737233 chr13 115169878 2590429 0.02249224402234758 0.3255009456542916 chr14 107349540 2867301 0.02670995143528328 0.36794078994203877 chr15 102531392 2459169 0.02398454709363548 0.4295155355185185 chr16 90354753 1867080 0.020663882507652918 0.3156174293500235 chr17 81195210 1924893 0.023706977295828165 0.32890555595478643 chr18 78077248 2223313 0.02847581154499708 0.6338861304446981 chr19 59128983 1618170 0.02736678220898878 0.4483435090431857 chr20 63025520 1682329 0.02669282220916226 0.36117360643896257 chr21 48129895 1235463 0.025669347502212503 0.351111753303937 chr22 51304566 802347 0.01563890044406574 0.2479058616554187 chrMT 16571 66469 4.011164081829702 4.216701333848729 chrX 155270560 4899442 0.03155422380134393 0.40189428887667966 chrY 59373566 230459 0.0038815084814006287 0.14220414605118964