BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238283.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,648,121 number of mapped reads = 1,265,351 (76.78%) number of supplementary alignments = 13,817 (0.84%) number of secondary alignments = 0 number of mapped bases = 81,784,867 bp number of sequenced bases = 81,733,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,526 duplication rate = 9.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2029 >>>>>>> ACTG content number of A's = 22,606,558 bp (27.66%) number of C's = 15,777,020 bp (19.3%) number of T's = 25,109,190 bp (30.72%) number of G's = 18,218,802 bp (22.29%) number of N's = 21,906 bp (0.03%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 832,573 number of insertions = 6,636 mapped reads with insertion percentage = 0.52% number of deletions = 31,424 mapped reads with deletion percentage = 2.45% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.299X There is a 1.55% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 6210275 0.02491578546558566 0.3759259036936208 chr2 243199373 7005984 0.028807574269527413 0.3524383609775266 chr3 198022430 5336313 0.026948023009312632 0.25528423698224095 chr4 191154276 5001920 0.02616692707412938 0.26478085750854985 chr5 180915260 5259739 0.029072942768896333 0.26530832382016867 chr6 171115067 4856267 0.028380125053511507 0.29290308858074215 chr7 159138663 5220679 0.032805849323994885 0.3975775299321973 chr8 146364022 4189948 0.028626898487389203 0.34748678242801156 chr9 141213431 3144324 0.022266465574368774 0.264235024913434 chr10 135534747 3595435 0.02652777298503387 0.28997759037607823 chr11 135006516 3361074 0.02489564281475125 0.27398074848746284 chr12 133851895 3763340 0.028115702060101576 0.2616026084613197 chr13 115169878 2972403 0.02580885776400666 0.25530829513681447 chr14 107349540 2842445 0.02647840875703799 0.2884564349644012 chr15 102531392 2325974 0.022685481535255077 0.2697851510662066 chr16 90354753 2379895 0.02633945554585269 0.2554940888705795 chr17 81195210 2173476 0.026768524892047202 0.2620684261184094 chr18 78077248 2169049 0.027780807540757586 0.38446344552817685 chr19 59128983 1500189 0.025371466307817267 0.30850886524902915 chr20 63025520 1623132 0.025753567761122795 0.25231043876640463 chr21 48129895 1087282 0.022590574943078517 0.23938962172295997 chr22 51304566 965195 0.01881304287809393 0.20795952270944995 chrMT 16571 9330 0.5630318025466176 1.2601747514211157 chrX 155270560 4561907 0.029380373201462015 0.27632996119550207 chrY 59373566 229292 0.00386185326985413 0.11481383508623033