BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524419.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 5,299,908 number of mapped reads = 4,875,988 (92%) number of supplementary alignments = 22,970 (0.43%) number of secondary alignments = 0 number of mapped bases = 285,484,645 bp number of sequenced bases = 285,406,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 498,834 duplication rate = 7.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8662 >>>>>>> ACTG content number of A's = 71,123,812 bp (24.92%) number of C's = 55,110,043 bp (19.31%) number of T's = 90,389,794 bp (31.67%) number of G's = 68,752,553 bp (24.09%) number of N's = 29,866 bp (0.01%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,441,711 number of insertions = 23,007 mapped reads with insertion percentage = 0.47% number of deletions = 47,089 mapped reads with deletion percentage = 0.96% homopolymer indels = 40.15% >>>>>>> Coverage mean coverageData = 0.0922X std coverageData = 0.8362X There is a 6.84% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 23190628 0.09304140510045109 1.7338357908000823 chr2 243199373 24026483 0.09879335914241852 1.206411307994236 chr3 198022430 18356987 0.09270155406132527 0.40061648810927675 chr4 191154276 18102987 0.09470354197046578 0.7003154769130778 chr5 180915260 16737598 0.09251623107967785 0.3973651631616929 chr6 171115067 15925525 0.09306909835122819 0.481610107173911 chr7 159138663 15501270 0.0974073157822119 1.0807521891461236 chr8 146364022 14052777 0.09601250913971195 0.5556619611494878 chr9 141213431 11963319 0.0847179968313354 0.5720182190852992 chr10 135534747 14167305 0.10452895153152128 0.99009869988927 chr11 135006516 12988910 0.09620950443606736 0.6410262090358501 chr12 133851895 12936068 0.09664463846402772 0.427763985303298 chr13 115169878 8512611 0.07391351929712038 0.3565811809049516 chr14 107349540 8556434 0.07970629403721712 0.4044111527560815 chr15 102531392 8355617 0.08149325623122332 0.3742772639186721 chr16 90354753 8909068 0.09860098892639328 0.49009983559059395 chr17 81195210 8323900 0.1025171312445648 0.5019181956859775 chr18 78077248 7458479 0.09552691969880905 1.2201578845158034 chr19 59128983 6512701 0.11014397118922205 1.0845405118348614 chr20 63025520 6434235 0.10208935999258713 0.47281336712095123 chr21 48129895 3903497 0.08110337660200588 0.6343381787405356 chr22 51304566 3765706 0.07339904210475146 0.36181935956392286 chrMT 16571 20764 1.2530324060105003 1.55625006314263 chrX 155270560 15684638 0.1010148865309689 0.4921631861683148 chrY 59373566 1097138 0.01847855997061049 0.6404457785698112