BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004157.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 = 2,535,212 number of mapped reads = 2,149,069 (84.77%) number of supplementary alignments = 17,173 (0.68%) number of secondary alignments = 0 number of mapped bases = 141,843,598 bp number of sequenced bases = 141,790,698 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,858 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2835 >>>>>>> ACTG content number of A's = 38,691,283 bp (27.29%) number of C's = 26,564,072 bp (18.73%) number of T's = 44,260,436 bp (31.22%) number of G's = 32,253,021 bp (22.75%) number of N's = 21,886 bp (0.02%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,255,993 number of insertions = 10,460 mapped reads with insertion percentage = 0.48% number of deletions = 32,161 mapped reads with deletion percentage = 1.48% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.0458X std coverageData = 0.4201X There is a 3.88% of reference with a coverageData >= 1X There is a 0.5% 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 0.01% 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 11026471 0.04423848958033288 0.815477162523175 chr2 243199373 11663736 0.04795956443522574 0.4690688287723333 chr3 198022430 9298684 0.04695773100047303 0.24586252220464497 chr4 191154276 9431073 0.04933749428655208 0.2641176763820741 chr5 180915260 8772432 0.04848917664546374 0.2530419839269558 chr6 171115067 8221208 0.04804491003705711 0.2915165566133026 chr7 159138663 7573208 0.04758873712543381 0.6028140568587378 chr8 146364022 7482041 0.05111940009410236 0.49351314976587674 chr9 141213431 6171891 0.043706118860606116 0.3760566459508116 chr10 135534747 6516150 0.04807733916380867 0.3936833664705218 chr11 135006516 6512805 0.0482406715835849 0.3616982762968758 chr12 133851895 6170262 0.04609768132158308 0.2502423973225884 chr13 115169878 4321386 0.037521842299772165 0.22522331040664453 chr14 107349540 4644500 0.04326520635300347 0.2629722073937686 chr15 102531392 4208249 0.04104351767700569 0.23751277865927914 chr16 90354753 4102533 0.04540472818292138 0.2675531046534097 chr17 81195210 3684778 0.04538171648302899 0.2797225878653753 chr18 78077248 3760524 0.04816414635925693 0.6831674065452228 chr19 59128983 2889481 0.048867422597138194 0.5595641990746133 chr20 63025520 2827008 0.04485497303314594 0.246856210276118 chr21 48129895 1753206 0.03642654944499671 0.2379075311858744 chr22 51304566 1564060 0.030485785612142203 0.19796894096513343 chrMT 16571 185357 11.185625490314404 6.2399515495526305 chrX 155270560 8660614 0.05577756659085921 0.3097164039303914 chrY 59373566 401941 0.006769696130429491 0.18879766169320392