BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525028.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 = 1,177,217 number of mapped reads = 1,077,831 (91.56%) number of supplementary alignments = 4,175 (0.35%) number of secondary alignments = 0 number of mapped bases = 62,533,391 bp number of sequenced bases = 62,513,199 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,015 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2928 >>>>>>> ACTG content number of A's = 15,371,047 bp (24.59%) number of C's = 12,224,525 bp (19.56%) number of T's = 19,478,895 bp (31.16%) number of G's = 15,438,078 bp (24.7%) number of N's = 654 bp (0%) GC percentage = 44.25% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 308,499 number of insertions = 3,501 mapped reads with insertion percentage = 0.32% number of deletions = 12,161 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.39% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.1978X There is a 1.86% of reference with a coverageData >= 1X There is a 0.11% 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 5110313 0.02050270919886695 0.33271811175211174 chr2 243199373 5228527 0.02149893289404163 0.22812513399530907 chr3 198022430 4124901 0.02083047359836964 0.15412624892542123 chr4 191154276 3977513 0.020807868300053094 0.16945063706405553 chr5 180915260 3740982 0.020678089841619774 0.1528187813123575 chr6 171115067 3611771 0.021107264622115363 0.1777900839528454 chr7 159138663 3443309 0.021637161800209418 0.22286896750962604 chr8 146364022 3161365 0.021599331289215325 0.21026932713053267 chr9 141213431 2624122 0.018582665837217707 0.17118583994727146 chr10 135534747 3069497 0.022647306819409196 0.21217734531725818 chr11 135006516 2899441 0.021476304151127047 0.18777650207391827 chr12 133851895 2830817 0.021148875030869006 0.1556237521471921 chr13 115169878 1939516 0.01684047976503023 0.1374870454615024 chr14 107349540 1892121 0.01762579513615056 0.14386508620283125 chr15 102531392 1806357 0.017617599495771987 0.143702065511317 chr16 90354753 1837863 0.020340523757505044 0.15801530310341141 chr17 81195210 1697045 0.02090080190691052 0.16600464686293437 chr18 78077248 1638310 0.020983193465015572 0.26359111249071515 chr19 59128983 1322658 0.022369030091385134 0.2400951052359905 chr20 63025520 1340752 0.021273160459445634 0.15694929285117395 chr21 48129895 824530 0.017131348406224448 0.15323126072922544 chr22 51304566 765645 0.01492352552012622 0.12956054720070614 chrMT 16571 409 0.02468167280188281 0.15515311092460765 chrX 155270560 3452114 0.022232894632440305 0.1688218423856157 chrY 59373566 193513 0.0032592450317031657 0.10206020118778139