BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525031.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 = 918,281 number of mapped reads = 843,620 (91.87%) number of supplementary alignments = 3,257 (0.35%) number of secondary alignments = 0 number of mapped bases = 48,888,619 bp number of sequenced bases = 48,873,171 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,167 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3954 >>>>>>> ACTG content number of A's = 12,511,300 bp (25.6%) number of C's = 9,025,054 bp (18.47%) number of T's = 15,825,801 bp (32.38%) number of G's = 11,510,495 bp (23.55%) number of N's = 521 bp (0%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 240,797 number of insertions = 3,171 mapped reads with insertion percentage = 0.37% number of deletions = 9,311 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0158X std coverageData = 0.1687X There is a 1.47% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 3831224 0.015370970730700807 0.28041906571631986 chr2 243199373 4095409 0.016839718579373147 0.19059654460651046 chr3 198022430 3316102 0.016746092854228685 0.13648976881623132 chr4 191154276 3252776 0.017016496141577287 0.14914883587820274 chr5 180915260 3011681 0.01664691524639768 0.13651048108599842 chr6 171115067 2977221 0.017398941263307925 0.15641216189248774 chr7 159138663 2818894 0.01771344528639153 0.19694255480626263 chr8 146364022 2593005 0.017716136551645185 0.17721201927802302 chr9 141213431 1941775 0.013750639625773274 0.14161858119957266 chr10 135534747 2369811 0.017484896326991337 0.1790623146291908 chr11 135006516 2316210 0.017156283034516644 0.16389726207128485 chr12 133851895 2355331 0.017596545794140606 0.14112759397116195 chr13 115169878 1494015 0.012972272142200238 0.1202602387698409 chr14 107349540 1480326 0.013789774972487073 0.1277779976182317 chr15 102531392 1333511 0.013005880189357031 0.12331341727996202 chr16 90354753 1300099 0.01438882800111246 0.13241653232074818 chr17 81195210 1327980 0.016355398304900005 0.14299558255170847 chr18 78077248 1312212 0.01680658621574367 0.21177245771294084 chr19 59128983 901726 0.015250152366057099 0.1898378146900993 chr20 63025520 926316 0.014697474927616623 0.13069692206177855 chr21 48129895 672634 0.013975388892911568 0.13290059916457053 chr22 51304566 372449 0.00725956828092065 0.0897176842335039 chrMT 16571 9664 0.5831874962283508 0.8830632014373258 chrX 155270560 2729099 0.017576409848718264 0.1467065326879746 chrY 59373566 149149 0.002512043827719561 0.08202144110172954