BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524740.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 = 1,644,275 number of mapped reads = 1,505,537 (91.56%) number of supplementary alignments = 5,361 (0.33%) number of secondary alignments = 0 number of mapped bases = 86,678,343 bp number of sequenced bases = 86,649,456 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,228 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.657 >>>>>>> ACTG content number of A's = 20,924,172 bp (24.15%) number of C's = 16,867,139 bp (19.47%) number of T's = 27,270,906 bp (31.47%) number of G's = 21,576,626 bp (24.9%) number of N's = 10,613 bp (0.01%) GC percentage = 44.37% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 443,081 number of insertions = 5,869 mapped reads with insertion percentage = 0.39% number of deletions = 17,808 mapped reads with deletion percentage = 1.17% homopolymer indels = 42.78% >>>>>>> Coverage mean coverageData = 0.028X std coverageData = 0.2504X There is a 2.5% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 6947746 0.02787453837477099 0.35099141803925293 chr2 243199373 7328220 0.03013256123814102 0.3970755109617056 chr3 198022430 5679678 0.028681993246926624 0.18838566397185944 chr4 191154276 5558232 0.029077204634438834 0.2144165591307793 chr5 180915260 5195998 0.02872061759743208 0.18628822790735544 chr6 171115067 4928574 0.028802688660958184 0.20532326694619266 chr7 159138663 4703199 0.02955409396646747 0.3012581701539643 chr8 146364022 4394306 0.03002312959123247 0.23240260035849186 chr9 141213431 3684561 0.026092142750925723 0.21211048861782827 chr10 135534747 4239556 0.031280214807203645 0.293748282556289 chr11 135006516 3855507 0.028557932714892074 0.22099693863017864 chr12 133851895 3863236 0.028862019473090014 0.18961711574090373 chr13 115169878 2612866 0.022687060587144148 0.16618564575571504 chr14 107349540 2685363 0.025015132808207656 0.17813847523197981 chr15 102531392 2527190 0.024647963425679424 0.17264268113752962 chr16 90354753 2613255 0.028922164172149305 0.20630514717794057 chr17 81195210 2456819 0.030258176559922686 0.19952515185461583 chr18 78077248 2265497 0.029016096981287046 0.33433253628794696 chr19 59128983 1899741 0.03212876162608783 0.2853283212023802 chr20 63025520 1869227 0.02965825589380302 0.1958709195804029 chr21 48129895 1167919 0.024265978556570714 0.19035558539107927 chr22 51304566 1078426 0.021020078407836058 0.16044707751159604 chrMT 16571 30847 1.8615050389234205 1.7558977249897416 chrX 155270560 4802916 0.030932560557519726 0.2096067632257104 chrY 59373566 289464 0.004875300904109415 0.14108851890550622