BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525202.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 = 2,117,801 number of mapped reads = 1,946,749 (91.92%) number of supplementary alignments = 6,979 (0.33%) number of secondary alignments = 0 number of mapped bases = 114,349,971 bp number of sequenced bases = 114,313,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,695 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2172 >>>>>>> ACTG content number of A's = 28,815,943 bp (25.21%) number of C's = 21,349,735 bp (18.68%) number of T's = 36,623,473 bp (32.04%) number of G's = 27,521,227 bp (24.08%) number of N's = 2,936 bp (0%) GC percentage = 42.75% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 563,623 number of insertions = 7,264 mapped reads with insertion percentage = 0.37% number of deletions = 22,805 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.65% >>>>>>> Coverage mean coverageData = 0.0369X std coverageData = 0.3476X There is a 3.27% of reference with a coverageData >= 1X There is a 0.3% 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 11706898 0.04696838047195878 0.6555043073514244 chr2 243199373 9698488 0.03987875412820246 0.4514250876607815 chr3 198022430 8689348 0.043880625038284805 0.23381971918053007 chr4 191154276 6543598 0.034232025235993155 0.22311290221664185 chr5 180915260 5380771 0.029741941061246023 0.1897631736354634 chr6 171115067 7210146 0.04213624274243483 0.25660859189695895 chr7 159138663 8196050 0.051502569177673686 0.6109055401264323 chr8 146364022 6362330 0.04346922087177954 0.3115357907579805 chr9 141213431 3979397 0.028180017805813386 0.24613452408183165 chr10 135534747 5580145 0.04117132413284395 0.35953058600556087 chr11 135006516 4751722 0.03519624193546332 0.26172194749993727 chr12 133851895 5330310 0.03982244704118683 0.22434007385626123 chr13 115169878 2612099 0.022680400859676174 0.1714742580150627 chr14 107349540 4993254 0.04651397667842824 0.24308691160464654 chr15 102531392 2297282 0.022405645287640295 0.16828361349977736 chr16 90354753 2998089 0.033181309233394726 0.22573700212079206 chr17 81195210 2204956 0.027156232492039863 0.1911716719113562 chr18 78077248 2495559 0.031962691615360216 0.4369769045453845 chr19 59128983 1954241 0.033050475432665566 0.44180790133256714 chr20 63025520 2173331 0.03448334896721201 0.20750425433404335 chr21 48129895 1444356 0.030009539808885932 0.20449933608423293 chr22 51304566 939903 0.018320065313484964 0.14828378720405755 chrMT 16571 24554 1.4817452175487298 1.5107899871439086 chrX 155270560 6455755 0.04157745679541569 0.24465860249602717 chrY 59373566 327389 0.00551405317309053 0.1628084052015851