BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716337.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 = 532,536 number of mapped reads = 468,275 (87.93%) number of supplementary alignments = 2,103 (0.39%) number of secondary alignments = 0 number of mapped bases = 26,734,582 bp number of sequenced bases = 26,727,073 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,142 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5932 >>>>>>> ACTG content number of A's = 7,221,859 bp (27.02%) number of C's = 4,737,626 bp (17.73%) number of T's = 8,357,602 bp (31.27%) number of G's = 6,409,589 bp (23.98%) number of N's = 397 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 149,842 number of insertions = 2,229 mapped reads with insertion percentage = 0.47% number of deletions = 4,485 mapped reads with deletion percentage = 0.95% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.0086X std coverageData = 0.1136X There is a 0.82% of reference with a coverageData >= 1X There is a 0.03% 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 2134018 0.008561735940469332 0.16807583487322147 chr2 243199373 2251584 0.009258181763486702 0.12098557771655416 chr3 198022430 1786572 0.009022068863613076 0.09779148145095468 chr4 191154276 1789293 0.009360465470309437 0.10466127350639447 chr5 180915260 1636943 0.009048120097773952 0.09816926719456211 chr6 171115067 1563074 0.00913463686982047 0.10150048400540362 chr7 159138663 1475010 0.009268709263945494 0.1194426550011665 chr8 146364022 1354955 0.009257432130417952 0.12168545405954392 chr9 141213431 1133533 0.008027090567610385 0.11216705309346384 chr10 135534747 1278431 0.009432496302959122 0.12056168242447239 chr11 135006516 1193867 0.00884303243556037 0.10909113403685007 chr12 133851895 1220266 0.00911653884317439 0.10001827611557075 chr13 115169878 871123 0.007563809349524535 0.08925442952066495 chr14 107349540 794006 0.00739645460986605 0.09101688830863536 chr15 102531392 760281 0.007415104634490869 0.0886710684508337 chr16 90354753 758274 0.008392187182449605 0.09867241402933405 chr17 81195210 683449 0.008417356146994386 0.09706743160603969 chr18 78077248 725443 0.009291349510679475 0.1660664314840264 chr19 59128983 518299 0.00876556594927398 0.13071734541100954 chr20 63025520 546776 0.008675469873156144 0.09736568638361638 chr21 48129895 363165 0.0075455182272888815 0.09190362170108327 chr22 51304566 279986 0.005457331029756689 0.07598561228502718 chrMT 16571 464 0.028000724156659225 0.17560599904183694 chrX 155270560 1533420 0.009875793582505274 0.1088934950572603 chrY 59373566 82350 0.001386980866198941 0.04837367633669596