BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004039.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 = 2,446,942 number of mapped reads = 2,007,247 (82.03%) number of supplementary alignments = 29,045 (1.19%) number of secondary alignments = 0 number of mapped bases = 130,491,683 bp number of sequenced bases = 130,405,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 248,465 duplication rate = 9.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3943 >>>>>>> ACTG content number of A's = 36,866,924 bp (28.27%) number of C's = 22,913,011 bp (17.57%) number of T's = 42,722,066 bp (32.76%) number of G's = 27,816,909 bp (21.33%) number of N's = 86,500 bp (0.07%) GC percentage = 38.9% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,208,330 number of insertions = 10,262 mapped reads with insertion percentage = 0.51% number of deletions = 50,244 mapped reads with deletion percentage = 2.46% homopolymer indels = 43.3% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.414X There is a 2.41% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 11035058 0.044272940848560614 0.6431317100107445 chr2 243199373 12061097 0.049593454338387626 0.4693289955579394 chr3 198022430 7582621 0.03829172786133369 0.31168857390280474 chr4 191154276 15466684 0.08091204823479858 0.4872360502173922 chr5 180915260 14554101 0.08044706123739921 0.455412659901171 chr6 171115067 6735844 0.039364412018726556 0.3202457792581997 chr7 159138663 6045102 0.037986381725476734 0.33977206872779836 chr8 146364022 4615940 0.031537395166689255 0.5639569922315271 chr9 141213431 8918502 0.0631561880257693 0.4801279377772386 chr10 135534747 2110888 0.01557451536763484 0.3681031184213459 chr11 135006516 3087827 0.022871688652420303 0.2437259114089547 chr12 133851895 7395589 0.05525203061189384 0.38450143451092517 chr13 115169878 2537502 0.02203268809575365 0.23364440067120013 chr14 107349540 4006066 0.037317961492895076 0.33166674724753986 chr15 102531392 1829307 0.017841433382665868 0.21403766756354606 chr16 90354753 2574685 0.028495291221702527 0.29850345456567634 chr17 81195210 1147440 0.014131868123747693 0.19098670123015324 chr18 78077248 2883472 0.036931014781668534 0.5579981679153989 chr19 59128983 2714517 0.045908399946604866 0.47539871789932964 chr20 63025520 1980877 0.03142976051605762 0.2833425855074341 chr21 48129895 1280991 0.026615287650222384 0.2989217047108614 chr22 51304566 1370620 0.026715360968066662 0.24966094860998203 chrMT 16571 15540 0.9377828736950093 1.518599351474541 chrX 155270560 8209097 0.05286962963230119 0.38604199628376634 chrY 59373566 332316 0.005597036229893957 0.1884640705372614