BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082906.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,152,426 number of mapped reads = 1,930,998 (89.71%) number of supplementary alignments = 20,797 (0.97%) number of secondary alignments = 0 number of mapped bases = 128,735,927 bp number of sequenced bases = 128,685,625 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,324 duplication rate = 4.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.997 >>>>>>> ACTG content number of A's = 35,307,580 bp (27.44%) number of C's = 23,758,139 bp (18.46%) number of T's = 40,859,788 bp (31.75%) number of G's = 28,754,342 bp (22.34%) number of N's = 5,776 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 926,742 number of insertions = 9,853 mapped reads with insertion percentage = 0.51% number of deletions = 30,230 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.43% >>>>>>> Coverage mean coverageData = 0.0416X std coverageData = 0.3355X There is a 3.47% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12772272 0.05124268877949957 0.540479614159152 chr2 243199373 10465488 0.04303254515380679 0.4178529562369081 chr3 198022430 9181204 0.046364464874004425 0.2489493562823507 chr4 191154276 6760135 0.0353648118235137 0.22013264659560178 chr5 180915260 7746922 0.04282072170141977 0.24092607311790676 chr6 171115067 9079805 0.05306256870997807 0.32489341910456354 chr7 159138663 7562321 0.04752032508907028 0.42821565892429614 chr8 146364022 9681701 0.06614809341601723 0.4781539612753346 chr9 141213431 3439031 0.024353427118416236 0.2546523931444304 chr10 135534747 4147036 0.03059758542951351 0.2504553815207775 chr11 135006516 6488139 0.048057969290904445 0.35569794558358464 chr12 133851895 3969392 0.029655104994964772 0.20263896366908754 chr13 115169878 3736802 0.0324460012018073 0.20950288154573501 chr14 107349540 3851753 0.035880479785940396 0.22952905392895362 chr15 102531392 2440279 0.023800310835534154 0.18214240663412098 chr16 90354753 4142986 0.0458524412102593 0.2551313670821973 chr17 81195210 2260381 0.027838846651175603 0.22611535439280908 chr18 78077248 3300455 0.042271661521676586 0.49901392917966886 chr19 59128983 2350158 0.03974629497686439 0.41175894358139814 chr20 63025520 2640899 0.041902058086946366 0.24423739932174104 chr21 48129895 2571527 0.05342889279106053 0.27797668929596603 chr22 51304566 1327836 0.025881439090625968 0.18347434185217124 chrMT 16571 211195 12.744855470400097 7.660605945192035 chrX 155270560 8327126 0.05362978017210732 0.28657552155416915 chrY 59373566 281084 0.00473416065324424 0.0971280587709961