BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230347.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,295,878 number of mapped reads = 1,843,685 (80.3%) number of supplementary alignments = 10,938 (0.48%) number of secondary alignments = 0 number of mapped bases = 120,164,431 bp number of sequenced bases = 120,106,619 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,539 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8873 >>>>>>> ACTG content number of A's = 32,786,732 bp (27.3%) number of C's = 20,393,075 bp (16.98%) number of T's = 40,326,462 bp (33.58%) number of G's = 26,372,720 bp (21.96%) number of N's = 227,630 bp (0.19%) GC percentage = 38.94% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,133,907 number of insertions = 10,633 mapped reads with insertion percentage = 0.57% number of deletions = 35,317 mapped reads with deletion percentage = 1.89% homopolymer indels = 47.32% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3946X There is a 3.42% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 11798285 0.04733502750229858 0.801596271271884 chr2 243199373 7969033 0.03276748990631649 0.32055776946407266 chr3 198022430 11154740 0.05633068940725553 0.26546547822899835 chr4 191154276 10133431 0.053011793468852354 0.25972996719598646 chr5 180915260 6729406 0.03719645319029473 0.21292151223622585 chr6 171115067 6178382 0.036106592530510476 0.2663659174749601 chr7 159138663 7878430 0.04950669970125362 0.49248951115997 chr8 146364022 5259346 0.03593332519927609 0.742233770645785 chr9 141213431 4106897 0.02908290642693895 0.3085215656839269 chr10 135534747 4739043 0.03496552068673578 0.4253726185373487 chr11 135006516 4335008 0.03210962054601868 0.26124745334554295 chr12 133851895 5329973 0.03981992933308864 0.22352758508560652 chr13 115169878 4011234 0.03482884648015343 0.20344293809030564 chr14 107349540 2920950 0.027209711378362682 0.1957766583157942 chr15 102531392 3543670 0.03456180522741757 0.2023768364911917 chr16 90354753 2109146 0.023342944670547656 0.1924715572715631 chr17 81195210 2961518 0.03647404816121542 0.21980757877579624 chr18 78077248 3179300 0.040719929063073534 0.5134900643174127 chr19 59128983 2013658 0.03405534642799454 0.4531600661545586 chr20 63025520 1824230 0.02894430700452769 0.19390414030434017 chr21 48129895 1346981 0.027986368970885973 0.19796430533562145 chr22 51304566 1080389 0.021058340109533332 0.15739416947862356 chrMT 16571 196105 11.834228471425986 6.728874846051804 chrX 155270560 9058004 0.058336905592405924 0.2976453471395395 chrY 59373566 307272 0.005175232358453929 0.10777385064726208