BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716953.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,824,480 number of mapped reads = 1,626,847 (89.17%) number of supplementary alignments = 7,641 (0.42%) number of secondary alignments = 0 number of mapped bases = 93,646,099 bp number of sequenced bases = 93,619,681 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,582 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7864 >>>>>>> ACTG content number of A's = 24,156,287 bp (25.8%) number of C's = 18,734,434 bp (20.01%) number of T's = 28,800,429 bp (30.76%) number of G's = 21,927,338 bp (23.42%) number of N's = 1,193 bp (0%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 469,134 number of insertions = 7,205 mapped reads with insertion percentage = 0.44% number of deletions = 16,992 mapped reads with deletion percentage = 1.04% homopolymer indels = 40.86% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.2739X There is a 2.7% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 10505631 0.04214886589991686 0.4995742270301606 chr2 243199373 7668993 0.031533769620368225 0.32463866703085326 chr3 198022430 8154283 0.04117858264844038 0.22467602238297824 chr4 191154276 4217190 0.02206170894131607 0.17202005173045 chr5 180915260 4068008 0.022485709607912567 0.16545028594686254 chr6 171115067 7788995 0.045519048302157986 0.30065042116057744 chr7 159138663 5269986 0.03311568603539166 0.3289516598138713 chr8 146364022 7320500 0.05001570672880252 0.27072420160166655 chr9 141213431 3818436 0.027040175803107566 0.24019500769292793 chr10 135534747 4676063 0.03450084279863672 0.31146839681977434 chr11 135006516 3024896 0.022405555595553624 0.2140629896276899 chr12 133851895 4342979 0.032446152518049894 0.20420546999755235 chr13 115169878 2108745 0.01830986570985167 0.14884939326124597 chr14 107349540 1976734 0.018413995998492402 0.18651824874507936 chr15 102531392 2741962 0.026742658482584534 0.18467958165176626 chr16 90354753 2006712 0.0222092577686533 0.18344428455691558 chr17 81195210 2120906 0.026121072905655397 0.1855817797942753 chr18 78077248 1734701 0.02221775285932209 0.3809157226468593 chr19 59128983 2519093 0.0426033540945563 0.36719191157944864 chr20 63025520 1546952 0.024544851038119164 0.17492952197662404 chr21 48129895 833537 0.017318487813031795 0.16531034081065069 chr22 51304566 1112854 0.021691129791449753 0.16168887180612218 chrMT 16571 90224 5.444692535151771 3.5874124890195103 chrX 155270560 3794808 0.024439971105919885 0.20330064255717295 chrY 59373566 202911 0.0034175309598214127 0.08868075286076642