BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716849.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 = 738,545 number of mapped reads = 626,396 (84.81%) number of supplementary alignments = 3,405 (0.46%) number of secondary alignments = 0 number of mapped bases = 35,955,792 bp number of sequenced bases = 35,946,254 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,839 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5124 >>>>>>> ACTG content number of A's = 9,311,924 bp (25.91%) number of C's = 6,935,670 bp (19.29%) number of T's = 11,288,649 bp (31.4%) number of G's = 8,409,754 bp (23.4%) number of N's = 257 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 174,739 number of insertions = 2,566 mapped reads with insertion percentage = 0.41% number of deletions = 6,190 mapped reads with deletion percentage = 0.98% homopolymer indels = 42.01% >>>>>>> Coverage mean coverageData = 0.0116X std coverageData = 0.1342X There is a 1.09% of reference with a coverageData >= 1X There is a 0.06% 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 4310751 0.017294845576332585 0.19910400726812386 chr2 243199373 3719337 0.015293365908472141 0.1833836551942036 chr3 198022430 2337653 0.011804990980062208 0.11403201453122694 chr4 191154276 1516648 0.007934156806411173 0.10090566702977687 chr5 180915260 2598794 0.014364703121229243 0.12621985948714956 chr6 171115067 1367950 0.007994328167489774 0.09814638915942317 chr7 159138663 1889469 0.011873098368307895 0.15595238727945976 chr8 146364022 1636561 0.011181443210135342 0.13026227875884755 chr9 141213431 1011910 0.007165819800809174 0.10299403611033935 chr10 135534747 1635272 0.012065334065219452 0.12357897784091297 chr11 135006516 1543058 0.011429507595026006 0.1312370482223855 chr12 133851895 1403069 0.010482249803037903 0.10800135097419981 chr13 115169878 1050439 0.009120778959234462 0.09990791006246261 chr14 107349540 772502 0.0071961370304893715 0.09039639782330694 chr15 102531392 1605584 0.015659438233316874 0.13221368927352575 chr16 90354753 1094348 0.01211168160683257 0.11771854448794104 chr17 81195210 1384472 0.017051153633323938 0.1418540604595839 chr18 78077248 1186182 0.015192415593336487 0.19728712032701418 chr19 59128983 578178 0.009778250371733943 0.1386622745558982 chr20 63025520 968740 0.015370599084307436 0.1306213710265739 chr21 48129895 458126 0.009518533127903146 0.10361221063588637 chr22 51304566 429746 0.008376369463879686 0.09661694910298721 chrMT 16571 5055 0.305050992698087 0.6083217602074945 chrX 155270560 1364256 0.008786314675492894 0.10429975604694479 chrY 59373566 87692 0.001476953565497481 0.04628692157502969