BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819002.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,355,235 number of mapped reads = 1,324,806 (97.75%) number of supplementary alignments = 20,916 (1.54%) number of secondary alignments = 0 number of mapped bases = 122,569,296 bp number of sequenced bases = 122,497,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 534,669 duplication rate = 33.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2213 >>>>>>> ACTG content number of A's = 35,391,179 bp (28.89%) number of C's = 25,693,191 bp (20.97%) number of T's = 35,152,570 bp (28.7%) number of G's = 26,254,421 bp (21.43%) number of N's = 6,231 bp (0.01%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 776,554 number of insertions = 20,706 mapped reads with insertion percentage = 1.52% number of deletions = 38,573 mapped reads with deletion percentage = 2.84% homopolymer indels = 40.98% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.5191X There is a 2.04% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 12714059 0.05100913670341467 0.9560070912520147 chr2 243199373 10300965 0.0423560508110356 0.674629110804704 chr3 198022430 6423423 0.03243785565099873 0.30798153251613697 chr4 191154276 7194994 0.03763972300572549 0.3930448354906428 chr5 180915260 6862778 0.03793366021196885 0.3446360811769023 chr6 171115067 5002291 0.029233492337644353 0.3339682871509516 chr7 159138663 5758505 0.03618545544774371 0.6284610580769914 chr8 146364022 11220431 0.07666112782825824 0.5082531998956634 chr9 141213431 5336840 0.03779272242170789 0.431819198635035 chr10 135534747 6591290 0.048631735742274265 0.6641281993673865 chr11 135006516 4218545 0.031246973294237146 0.3378413233930694 chr12 133851895 5370708 0.04012425823332572 0.3494391682821373 chr13 115169878 2305064 0.02001446940839861 0.24237082029176932 chr14 107349540 2268973 0.021136308548690568 0.26728878730699474 chr15 102531392 3290401 0.03209164467405261 0.3169336185417523 chr16 90354753 3928561 0.04347929543894608 0.539638601938669 chr17 81195210 4066711 0.0500856023403351 0.4271886787293604 chr18 78077248 2830410 0.03625140578725316 0.49075695052280577 chr19 59128983 2466993 0.04172222951982787 0.7746439547209134 chr20 63025520 3527547 0.05597013717617879 0.4366684044342414 chr21 48129895 1648590 0.03425293157194712 0.37032235602658725 chr22 51304566 923268 0.017995825166906197 0.2429865205251117 chrMT 16571 26118 1.5761269688009172 2.319472197669786 chrX 155270560 7801883 0.05024702042679565 0.42692805639273906 chrY 59373566 489948 0.008251955087218443 0.542654111523412