BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716758.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 = 405,669 number of mapped reads = 344,337 (84.88%) number of supplementary alignments = 1,496 (0.37%) number of secondary alignments = 0 number of mapped bases = 20,293,050 bp number of sequenced bases = 20,286,653 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,021 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7137 >>>>>>> ACTG content number of A's = 5,328,936 bp (26.27%) number of C's = 3,862,018 bp (19.04%) number of T's = 6,122,085 bp (30.18%) number of G's = 4,973,071 bp (24.51%) number of N's = 543 bp (0%) GC percentage = 43.55% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 102,328 number of insertions = 1,589 mapped reads with insertion percentage = 0.46% number of deletions = 3,985 mapped reads with deletion percentage = 1.15% homopolymer indels = 43% >>>>>>> Coverage mean coverageData = 0.0066X std coverageData = 0.0937X There is a 0.63% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1639839 0.006579076888237723 0.1344934889997861 chr2 243199373 1717616 0.007062583997698053 0.10245819610204521 chr3 198022430 1327559 0.006704083976749503 0.08390476360799616 chr4 191154276 1317174 0.0068906331972401185 0.08669494763224016 chr5 180915260 1222419 0.0067568595374431105 0.08415758355335516 chr6 171115067 1170451 0.006840139915908165 0.08910997831963208 chr7 159138663 1126332 0.0070776766548553945 0.10284712050539231 chr8 146364022 1031982 0.007050790118352993 0.09689954263077727 chr9 141213431 833590 0.005903050397522032 0.0842615163312273 chr10 135534747 997277 0.007358090984594526 0.09985267697540036 chr11 135006516 936455 0.00693636890829773 0.09081300401748041 chr12 133851895 910104 0.006799335937679478 0.08483825406844349 chr13 115169878 650394 0.0056472578706734415 0.07677455305598865 chr14 107349540 607164 0.005655953439576918 0.07786317939146777 chr15 102531392 585155 0.0057070813980561194 0.07752865642076313 chr16 90354753 584648 0.006470583788768699 0.08442021123759887 chr17 81195210 543856 0.006698129113774076 0.08569385474679721 chr18 78077248 543014 0.006954830170243705 0.10730349324449692 chr19 59128983 417963 0.007068665463094469 0.10938202293577876 chr20 63025520 420448 0.006671075462764925 0.08405404216806843 chr21 48129895 264293 0.005491244059435409 0.07756940219230755 chr22 51304566 237478 0.004628788790455805 0.06950305831278568 chrMT 16571 906 0.05467382777140788 0.23823034429475587 chrX 155270560 1141957 0.0073546266594259726 0.08999546965360689 chrY 59373566 64976 0.001094359062078232 0.04152634101276376