BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013244.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 = 1,929,378 number of mapped reads = 1,662,593 (86.17%) number of supplementary alignments = 22,223 (1.15%) number of secondary alignments = 0 number of mapped bases = 107,442,736 bp number of sequenced bases = 107,355,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 138,584 duplication rate = 6.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1592 >>>>>>> ACTG content number of A's = 30,480,655 bp (28.39%) number of C's = 18,756,684 bp (17.47%) number of T's = 35,287,060 bp (32.87%) number of G's = 22,806,368 bp (21.24%) number of N's = 24,434 bp (0.02%) GC percentage = 38.72% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,007,135 number of insertions = 7,542 mapped reads with insertion percentage = 0.45% number of deletions = 50,078 mapped reads with deletion percentage = 2.96% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.0347X std coverageData = 0.408X There is a 2.41% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 11794815 0.04732110577168833 0.8800595710470086 chr2 243199373 12115397 0.049816727940330666 0.4149452044294291 chr3 198022430 5232761 0.026425092349386885 0.21869338861050755 chr4 191154276 8835945 0.04622415561344806 0.29254285282385967 chr5 180915260 5568544 0.03077984687416639 0.24078473138976245 chr6 171115067 4010459 0.02343720556179895 0.2427033165873909 chr7 159138663 8932116 0.056127881381031836 0.6217960594806627 chr8 146364022 4341682 0.029663587681404383 0.513721599403705 chr9 141213431 760413 0.005384848980831009 0.17862780974988512 chr10 135534747 4715486 0.034791712858695936 0.3605175628639466 chr11 135006516 4792066 0.03549507195637876 0.2972902450118168 chr12 133851895 6777669 0.05063558495006738 0.3062809517181059 chr13 115169878 1679572 0.014583431268373836 0.16111415551518446 chr14 107349540 3892547 0.036260490729629585 0.2624099844986384 chr15 102531392 2436505 0.02376350259635605 0.20472074700835005 chr16 90354753 4184018 0.0463065623122228 0.3104526577451585 chr17 81195210 1298844 0.01599655940295 0.19286983726610427 chr18 78077248 2003855 0.025665031124047815 0.42678685233021685 chr19 59128983 1731351 0.029280919646461703 0.6041968953494995 chr20 63025520 1442522 0.022887903185884066 0.2083300998301925 chr21 48129895 3046772 0.06330310922141011 0.3454867437715268 chr22 51304566 964742 0.018804213254625328 0.17829179068460999 chrMT 16571 10199 0.615472813952085 1.0709270183410438 chrX 155270560 6624951 0.04266714179429765 0.2965905044574339 chrY 59373566 249505 0.004202290965646227 0.09000157741949355