BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124930.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,790,414 number of mapped reads = 4,734,132 (98.83%) number of supplementary alignments = 20,534 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,369,813 number of mapped paired reads (second in pair) = 2,364,319 number of mapped paired reads (both in pair) = 4,713,806 number of mapped paired reads (singletons) = 20,326 number of mapped bases = 431,249,796 bp number of sequenced bases = 431,020,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 332,599 duplication rate = 3.27% >>>>>>> Insert size mean insert size = 72,596.0912 std insert size = 2,562,455.8911 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 52.5285 >>>>>>> ACTG content number of A's = 123,736,834 bp (28.71%) number of C's = 83,956,666 bp (19.48%) number of T's = 128,664,570 bp (29.85%) number of G's = 94,379,082 bp (21.9%) number of N's = 282,964 bp (0.07%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 4,048,029 number of insertions = 64,134 mapped reads with insertion percentage = 1.32% number of deletions = 135,488 mapped reads with deletion percentage = 2.81% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.1393X std coverageData = 2.2287X There is a 9.1% of reference with a coverageData >= 1X There is a 2.86% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 39796341 0.1596639592725428 2.112025052656437 chr2 243199373 37412093 0.15383301584416503 2.3536629199583077 chr3 198022430 32024174 0.1617199324339167 0.6773831370824704 chr4 191154276 20004923 0.10465328539132444 1.661623070458593 chr5 180915260 18971428 0.10486361404781443 0.4291044746262691 chr6 171115067 26018829 0.15205457623436514 0.9423163572877317 chr7 159138663 19982242 0.12556497348479043 3.2102193464077593 chr8 146364022 29314078 0.20028199279738296 0.8769502045471382 chr9 141213431 23604351 0.16715372491728495 2.627888436848399 chr10 135534747 29918620 0.2207450167741856 7.247750218984893 chr11 135006516 18492672 0.13697614417366344 0.7845243046531648 chr12 133851895 15703758 0.11732189521859217 0.4534216622266378 chr13 115169878 13222842 0.1148116350353345 0.4350528449924859 chr14 107349540 13757367 0.12815487611777376 0.5492290098397117 chr15 102531392 7316202 0.07135572683924939 0.34410659266003574 chr16 90354753 13585464 0.1503569380572597 3.536164326344254 chr17 81195210 8568575 0.10553054792271613 0.966248033727268 chr18 78077248 11563503 0.14810336296689144 2.5437814654857775 chr19 59128983 5735584 0.09700122865296026 1.1789377759094875 chr20 63025520 11948870 0.18958780506689987 0.7117864334743108 chr21 48129895 5340732 0.11096496262873626 0.8372726050726672 chr22 51304566 5075123 0.09892146831531524 0.42091953317764685 chrMT 16571 50676 3.0581135719027217 2.228929803364849 chrX 155270560 22643023 0.14582946696398855 0.6985083197188352 chrY 59373566 1198326 0.020182820078551454 1.5412950260672096