BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708633.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,259,773 number of mapped reads = 2,371,137 (72.74%) number of supplementary alignments = 703 (0.02%) number of secondary alignments = 0 number of mapped bases = 115,537,854 bp number of sequenced bases = 115,516,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,650 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0966 >>>>>>> ACTG content number of A's = 34,102,032 bp (29.52%) number of C's = 21,638,332 bp (18.73%) number of T's = 36,641,825 bp (31.72%) number of G's = 23,124,639 bp (20.02%) number of N's = 10,156 bp (0.01%) GC percentage = 38.75% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 724,565 number of insertions = 5,125 mapped reads with insertion percentage = 0.22% number of deletions = 13,817 mapped reads with deletion percentage = 0.58% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.0373X std coverageData = 0.3295X There is a 3.1% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% 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 7802137 0.031302377377025674 0.45660718080215645 chr2 243199373 11905955 0.04895553328585267 0.38355342315636926 chr3 198022430 10569518 0.053375357528942555 0.27052611356100237 chr4 191154276 10261814 0.053683413286553947 0.2724501336596793 chr5 180915260 7723149 0.04268931763965074 0.24408761073305232 chr6 171115067 8716777 0.050941025549784 0.3177752302938202 chr7 159138663 6072883 0.03816095275351157 0.5809764759278884 chr8 146364022 8161062 0.05575866178369982 0.5148217408971537 chr9 141213431 4222604 0.029902283161719934 0.26818552273818436 chr10 135534747 6440934 0.047522381843528284 0.3315500266076582 chr11 135006516 5568387 0.041245320336982846 0.37793087380587714 chr12 133851895 6866574 0.051299789218523954 0.2767878888979201 chr13 115169878 2518272 0.021865717353629566 0.17313221188195163 chr14 107349540 1135407 0.01057672906656144 0.14153883300429046 chr15 102531392 843402 0.008225792935689393 0.1069693253577658 chr16 90354753 966418 0.01069581807168462 0.1261374991739515 chr17 81195210 3258910 0.04013672727738496 0.30660152380714495 chr18 78077248 3170545 0.04060779652479555 0.3254143992753257 chr19 59128983 1792108 0.030308452962906532 0.3429542095079879 chr20 63025520 3024242 0.04798440377802515 0.2569907293767683 chr21 48129895 212796 0.0044212853570530335 0.10838164911547093 chr22 51304566 1167161 0.022749651561227515 0.17473614198374612 chrMT 16571 4184 0.2524892885160823 0.57932853955821 chrX 155270560 2996992 0.01930174013670074 0.199259643112375 chrY 59373566 135623 0.002284232009914985 0.06277793946066976