BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238311.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 = 2,224,211 number of mapped reads = 1,637,471 (73.62%) number of supplementary alignments = 21,583 (0.97%) number of secondary alignments = 0 number of mapped bases = 102,483,645 bp number of sequenced bases = 102,429,496 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 271,295 duplication rate = 11.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3166 >>>>>>> ACTG content number of A's = 28,317,680 bp (27.65%) number of C's = 19,986,176 bp (19.51%) number of T's = 31,104,006 bp (30.37%) number of G's = 22,999,938 bp (22.45%) number of N's = 21,696 bp (0.02%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 936,602 number of insertions = 8,245 mapped reads with insertion percentage = 0.5% number of deletions = 32,917 mapped reads with deletion percentage = 1.98% homopolymer indels = 44.14% >>>>>>> Coverage mean coverageData = 0.0331X std coverageData = 0.4615X There is a 1.64% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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% 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 11265324 0.04519677405337337 0.4788849854584416 chr2 243199373 5640368 0.023192362424388324 0.6791974160780315 chr3 198022430 3406539 0.017202793643124166 0.25049363394107266 chr4 191154276 7437427 0.03890798132080498 0.3928626276753614 chr5 180915260 2188156 0.012094922230440926 0.22341860819395978 chr6 171115067 5387448 0.03148435783273252 0.414524001921831 chr7 159138663 2047035 0.012863216024379946 0.24536379274805079 chr8 146364022 11368845 0.07767513385222496 0.7732575842831144 chr9 141213431 3852255 0.027279664354306354 0.36535383164277796 chr10 135534747 1910948 0.014099321703828466 0.2403520453101113 chr11 135006516 4030745 0.029855929324181657 0.34131459043922546 chr12 133851895 2799194 0.020912621371553985 0.2779151536794319 chr13 115169878 5511424 0.04785473507230771 0.46048420597927686 chr14 107349540 679417 0.006329016407522566 0.599362683653168 chr15 102531392 5662824 0.055230148440781925 0.825565245647467 chr16 90354753 1245570 0.013785329035208585 0.2267429230838005 chr17 81195210 3354769 0.04131732647775651 0.3816560864578137 chr18 78077248 5337549 0.06836241205632658 0.5898469580791648 chr19 59128983 1605864 0.027158660922681523 0.37891465055000856 chr20 63025520 2930367 0.04649492776894185 0.4054505876497028 chr21 48129895 1822973 0.03787610590050113 0.3525860719358474 chr22 51304566 345772 0.006739595068399955 0.135864949332081 chrMT 16571 9268 0.5592903264739605 1.26470239578819 chrX 155270560 12310147 0.07928191281077365 0.5882085320936733 chrY 59373566 333417 0.005615579835646051 0.20208336141931874