BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013358.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 = 4,504,906 number of mapped reads = 965,238 (21.43%) number of supplementary alignments = 3,352 (0.07%) number of secondary alignments = 0 number of mapped bases = 52,391,305 bp number of sequenced bases = 52,371,273 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 132,598 duplication rate = 11.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3678 >>>>>>> ACTG content number of A's = 14,681,798 bp (28.03%) number of C's = 9,591,963 bp (18.32%) number of T's = 16,136,505 bp (30.81%) number of G's = 11,944,957 bp (22.81%) number of N's = 16,050 bp (0.03%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 489,100 number of insertions = 3,256 mapped reads with insertion percentage = 0.34% number of deletions = 12,562 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.2058X There is a 1.17% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.04% 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 3736766 0.014992002768169633 0.22905950019225776 chr2 243199373 5160495 0.02121919533073796 0.25494369679677154 chr3 198022430 4136292 0.020887997384942705 0.20194079928291547 chr4 191154276 3631668 0.0189986228715072 0.19954179948830258 chr5 180915260 2833442 0.015661708138937535 0.17357364799682481 chr6 171115067 3277966 0.01915650127992528 0.20946875365414264 chr7 159138663 3040552 0.019106306052099984 0.28276333210796323 chr8 146364022 3218456 0.021989392994406783 0.2707431723560977 chr9 141213431 2110755 0.014947268011638355 0.18495840331141503 chr10 135534747 1959107 0.014454647559861531 0.1849444100419442 chr11 135006516 2216340 0.01641654096162292 0.1858832469743885 chr12 133851895 2467592 0.01843524142859539 0.1890381098786158 chr13 115169878 1239218 0.010759914150469101 0.14410658480832578 chr14 107349540 2110511 0.019660177398058715 0.19724705241536855 chr15 102531392 1248971 0.012181352224302193 0.15930688649754834 chr16 90354753 1229927 0.01361220034545388 0.15907215410098624 chr17 81195210 1582663 0.019492073485615716 0.19333159177690382 chr18 78077248 1393003 0.017841343485876963 0.24029554139003312 chr19 59128983 830162 0.014039849121030883 0.1893218076729822 chr20 63025520 939185 0.01490166205689378 0.17225533635939366 chr21 48129895 780899 0.01622482243104831 0.1756866741843688 chr22 51304566 552156 0.01076231694465557 0.1389953352757025 chrMT 16571 45455 2.743045078752037 3.3321567199121023 chrX 155270560 2537182 0.01634039318206877 0.18244822475370448 chrY 59373566 112542 0.0018954899896024436 0.05496549923174952