BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524913.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 = 1,064,043 number of mapped reads = 986,475 (92.71%) number of supplementary alignments = 4,589 (0.43%) number of secondary alignments = 0 number of mapped bases = 57,647,318 bp number of sequenced bases = 57,628,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,910 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9542 >>>>>>> ACTG content number of A's = 14,200,901 bp (24.64%) number of C's = 11,373,928 bp (19.74%) number of T's = 18,018,007 bp (31.27%) number of G's = 14,035,445 bp (24.35%) number of N's = 486 bp (0%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 291,068 number of insertions = 3,836 mapped reads with insertion percentage = 0.39% number of deletions = 10,946 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.04% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.1959X There is a 1.67% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5843783 0.02344540999157631 0.34089046446420485 chr2 243199373 5118328 0.021045810837678435 0.22658890846164287 chr3 198022430 4039816 0.020400800050782125 0.15538057185866364 chr4 191154276 2599805 0.013600558953753145 0.15085185707798163 chr5 180915260 3513039 0.019418146374164346 0.1516604268243103 chr6 171115067 3682075 0.021518122656025374 0.16692519782948634 chr7 159138663 3476155 0.02184356041749578 0.23188297611115122 chr8 146364022 5058391 0.03456034434473248 0.26085339676182207 chr9 141213431 2049092 0.014510602748544507 0.16046111230142954 chr10 135534747 2509916 0.018518616484376513 0.20970549780857112 chr11 135006516 2886679 0.02138177538038238 0.1813389035774518 chr12 133851895 1891624 0.01413221680574638 0.13325575200159726 chr13 115169878 1362924 0.011834031811686038 0.11863834762311777 chr14 107349540 1046825 0.009751555525994802 0.11070739464865459 chr15 102531392 1504475 0.014673310979724142 0.13190463620420517 chr16 90354753 1708384 0.01890751668592354 0.15470057738407278 chr17 81195210 1279744 0.01576132385149321 0.1405193758675747 chr18 78077248 1481555 0.018975502312786434 0.24215918702750064 chr19 59128983 1174081 0.019856269132854865 0.24095929565593932 chr20 63025520 1093259 0.017346290835839197 0.14672892836148613 chr21 48129895 533747 0.011089718770423248 0.13721689911092727 chr22 51304566 1002082 0.019532023718902523 0.15399747537892922 chrMT 16571 13024 0.7859513608110554 1.1096601567745752 chrX 155270560 2605163 0.016778216037863197 0.15039488562007708 chrY 59373566 173352 0.0029196831465369624 0.10953933856813433