BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053675.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,320,293 number of mapped reads = 6,074,957 (73.01%) number of supplementary alignments = 211 (0%) number of secondary alignments = 0 number of mapped bases = 285,403,315 bp number of sequenced bases = 285,340,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,531,627 duplication rate = 18.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8147 >>>>>>> ACTG content number of A's = 87,258,277 bp (30.58%) number of C's = 54,606,034 bp (19.14%) number of T's = 86,110,141 bp (30.18%) number of G's = 57,285,605 bp (20.08%) number of N's = 80,928 bp (0.03%) GC percentage = 39.21% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,783,304 number of insertions = 13,298 mapped reads with insertion percentage = 0.22% number of deletions = 42,020 mapped reads with deletion percentage = 0.69% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.0922X std coverageData = 0.7753X There is a 4.01% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 26146477 0.10490034847295325 0.8550658765365818 chr2 243199373 23289278 0.09576208076819342 0.8877083067775531 chr3 198022430 20110937 0.10155888401127085 0.7640017348474584 chr4 191154276 17580340 0.09196937870225827 0.7478390464449628 chr5 180915260 17840832 0.09861430152437113 0.7541798264030766 chr6 171115067 16310884 0.09532114433850528 0.7743649071404253 chr7 159138663 15468055 0.0971985984323621 0.8311088916564995 chr8 146364022 14391499 0.09832675273162417 0.8377395281791624 chr9 141213431 11685304 0.08274923934112188 0.6999019245308086 chr10 135534747 13652897 0.10073355580174581 0.792078371258703 chr11 135006516 12742980 0.09438788865568533 0.7886427932474173 chr12 133851895 12854445 0.09603483760913509 0.750122871790796 chr13 115169878 9479999 0.08231318088224422 0.6798586406271528 chr14 107349540 7669103 0.07144048311711443 0.6696699629307769 chr15 102531392 8169675 0.07967974335118751 0.656932041033162 chr16 90354753 8025086 0.08881753016357645 0.7688850602446591 chr17 81195210 7213777 0.08884485919797486 0.6984683519888224 chr18 78077248 8337550 0.10678591028208372 0.838237341967697 chr19 59128983 5038685 0.08521514736690126 0.7751278984685219 chr20 63025520 5675179 0.09004573068179367 0.7239530744031838 chr21 48129895 3722984 0.07735283860477983 0.6986442036129147 chr22 51304566 3017652 0.05881839055026798 0.5570414416434499 chrMT 16571 314586 18.98412889988534 34.223430483597234 chrX 155270560 16016190 0.10315020439161166 0.8103707460153097 chrY 59373566 648921 0.010929459753183766 0.2371101270775603