BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238257.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 = 1,990,832 number of mapped reads = 1,691,531 (84.97%) number of supplementary alignments = 16,015 (0.8%) number of secondary alignments = 0 number of mapped bases = 108,765,876 bp number of sequenced bases = 108,702,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,374 duplication rate = 7.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8698 >>>>>>> ACTG content number of A's = 30,213,252 bp (27.79%) number of C's = 21,333,536 bp (19.63%) number of T's = 33,150,740 bp (30.5%) number of G's = 23,979,890 bp (22.06%) number of N's = 25,215 bp (0.02%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,012,522 number of insertions = 8,664 mapped reads with insertion percentage = 0.51% number of deletions = 36,915 mapped reads with deletion percentage = 2.16% homopolymer indels = 47.89% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.3213X There is a 2.14% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 10558327 0.04236028362793929 0.3740144247055983 chr2 243199373 9022075 0.03709744350368864 0.4064117454245384 chr3 198022430 6820490 0.034443017389494714 0.28317821609047406 chr4 191154276 6516676 0.034091186116077254 0.28498652047267886 chr5 180915260 6387537 0.03530678948807303 0.2860759269799279 chr6 171115067 7471179 0.04366172500753543 0.3425081222069178 chr7 159138663 5290786 0.033246389659563745 0.3907530613839511 chr8 146364022 8262753 0.056453443182915536 0.4141716085964572 chr9 141213431 3110909 0.022029837940840062 0.24901894336121758 chr10 135534747 6274132 0.04629168636733427 0.3422165776086717 chr11 135006516 4888026 0.03620585246418773 0.3221530287187902 chr12 133851895 4904106 0.03663830086230755 0.29214855659178013 chr13 115169878 2669113 0.023175443495737663 0.23387618355350456 chr14 107349540 3334318 0.031060384609007174 0.2924849642376394 chr15 102531392 2642249 0.025770146571305694 0.2763541669920707 chr16 90354753 3039210 0.033636415341647824 0.2782844752277303 chr17 81195210 3820894 0.047058120793086196 0.3415940579289269 chr18 78077248 2341146 0.029984996397414008 0.36525916378686096 chr19 59128983 1705692 0.028846970021452933 0.2996926231710156 chr20 63025520 2324678 0.03688470955892153 0.2935768267595391 chr21 48129895 1502343 0.031214341938622554 0.27048853909271164 chr22 51304566 1031428 0.020104019591550584 0.20875990687913276 chrMT 16571 45550 2.7487779856375596 3.119085054153374 chrX 155270560 4616175 0.029729879250773618 0.269491391648011 chrY 59373566 186084 0.0031341220097846237 0.07790611853871598