BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234137.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 = 791,897 number of mapped reads = 441,226 (55.72%) number of supplementary alignments = 1,771 (0.22%) number of secondary alignments = 0 number of mapped bases = 26,898,971 bp number of sequenced bases = 26,882,207 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,106 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2001 >>>>>>> ACTG content number of A's = 7,293,647 bp (27.13%) number of C's = 4,328,251 bp (16.1%) number of T's = 8,840,329 bp (32.89%) number of G's = 6,415,558 bp (23.87%) number of N's = 4,422 bp (0.02%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 272,748 number of insertions = 2,184 mapped reads with insertion percentage = 0.49% number of deletions = 9,595 mapped reads with deletion percentage = 2.14% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.0087X std coverageData = 0.112X There is a 0.81% of reference with a coverageData >= 1X There is a 0.04% 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 2161316 0.008671256229287388 0.12715558231899443 chr2 243199373 2192577 0.009015553670855887 0.11954895576665016 chr3 198022430 2017588 0.010188684180877894 0.10744910030409537 chr4 191154276 1604345 0.008392932837139358 0.09822771572098085 chr5 180915260 1622713 0.008969464488512466 0.1005657493797676 chr6 171115067 1643736 0.00960602727052668 0.1097799797298954 chr7 159138663 1561048 0.009809357264739619 0.13629564078049866 chr8 146364022 1405346 0.00960171755870442 0.16875933798240475 chr9 141213431 1082141 0.00766315917924266 0.09890227908409861 chr10 135534747 1270149 0.009371390201510467 0.10799348241385064 chr11 135006516 1266965 0.009384472968697304 0.11398836140034 chr12 133851895 1106844 0.008269169442838295 0.0966141010777874 chr13 115169878 1008496 0.008756595192364448 0.09971984681785369 chr14 107349540 1009580 0.009404604807808213 0.104352578097534 chr15 102531392 679691 0.006629101456069182 0.08695342364039872 chr16 90354753 672565 0.007443603990594717 0.09177392939437928 chr17 81195210 658724 0.008112843109833696 0.09680005087366485 chr18 78077248 663441 0.00849723852971867 0.14671623090200137 chr19 59128983 534967 0.00904745816446733 0.110325392618874 chr20 63025520 561906 0.008915531359360462 0.10089730487746981 chr21 48129895 379551 0.00788597190997404 0.09412046939384065 chr22 51304566 249259 0.0048584174749670425 0.07353589518733611 chrMT 16571 13457 0.8120813469313861 1.1253524412134086 chrX 155270560 1445134 0.009307198995096045 0.10501441998616688 chrY 59373566 87432 0.0014725745123680123 0.0431325227552659