BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068185.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 = 1,182,056 number of mapped reads = 992,083 (83.93%) number of supplementary alignments = 4,905 (0.41%) number of secondary alignments = 0 number of mapped bases = 62,072,125 bp number of sequenced bases = 62,038,705 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,117 duplication rate = 7.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4737 >>>>>>> ACTG content number of A's = 17,311,842 bp (27.9%) number of C's = 11,229,406 bp (18.1%) number of T's = 19,849,783 bp (32%) number of G's = 13,589,139 bp (21.9%) number of N's = 58,535 bp (0.09%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 607,238 number of insertions = 4,402 mapped reads with insertion percentage = 0.44% number of deletions = 19,579 mapped reads with deletion percentage = 1.95% homopolymer indels = 48.39% >>>>>>> Coverage mean coverageData = 0.0201X std coverageData = 0.2427X There is a 1.41% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 3430931 0.013764984762064043 0.26727583391756216 chr2 243199373 7004526 0.02880157918828187 0.2889826915448577 chr3 198022430 3276554 0.016546378104742982 0.17344475718361949 chr4 191154276 2868631 0.015006888990544998 0.16515144135578338 chr5 180915260 2274858 0.01257416317451607 0.15141071234323814 chr6 171115067 3071809 0.017951715496800757 0.23300081577830223 chr7 159138663 5087303 0.03196773746930374 0.48094031896840195 chr8 146364022 3170070 0.021658806287791134 0.2660004447631427 chr9 141213431 2436448 0.017253656275797166 0.21748978379056358 chr10 135534747 2527377 0.018647446916324712 0.22607006069872104 chr11 135006516 3119159 0.02310376633969282 0.24291968327730493 chr12 133851895 3145962 0.023503305649875184 0.20714173445939613 chr13 115169878 891591 0.007741529430117135 0.11743608240308762 chr14 107349540 2348820 0.021880112387999053 0.2052347449192579 chr15 102531392 1143668 0.011154320425104537 0.14105279796741216 chr16 90354753 2226490 0.024641647794665544 0.2177447090653491 chr17 81195210 2609911 0.03214365724283489 0.26924378173224944 chr18 78077248 977583 0.012520715381771652 0.25936035727708046 chr19 59128983 1128593 0.019086967891871233 0.23804881644384396 chr20 63025520 2268591 0.035994800201569144 0.2586655430693639 chr21 48129895 1473560 0.03061631445487259 0.23961731737489086 chr22 51304566 627937 0.012239397951441593 0.14277862118075463 chrMT 16571 7117 0.4294852453080683 0.9286998457597357 chrX 155270560 4815723 0.031015042387945273 0.2510196958015972 chrY 59373566 138913 0.0023396438745147967 0.06075078018517175