BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003993.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 = 4,467,749 number of mapped reads = 3,813,322 (85.35%) number of supplementary alignments = 25,291 (0.57%) number of secondary alignments = 0 number of mapped bases = 254,845,321 bp number of sequenced bases = 254,720,704 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 268,727 duplication rate = 5.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1851 >>>>>>> ACTG content number of A's = 71,757,140 bp (28.17%) number of C's = 45,000,868 bp (17.67%) number of T's = 83,990,235 bp (32.97%) number of G's = 53,944,243 bp (21.18%) number of N's = 28,218 bp (0.01%) GC percentage = 38.84% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 2,416,926 number of insertions = 22,385 mapped reads with insertion percentage = 0.58% number of deletions = 75,123 mapped reads with deletion percentage = 1.95% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.0823X std coverageData = 0.6973X There is a 5.92% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.14% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 26398482 0.10591139911342487 1.4055271405350196 chr2 243199373 20146760 0.08284050962582046 0.7693648238223301 chr3 198022430 19542397 0.09868779511492713 0.41375260022265936 chr4 191154276 11617588 0.060775977619250326 0.3529786516889146 chr5 180915260 8068996 0.044600969536787556 0.27979817533470674 chr6 171115067 14999076 0.0876549111832449 0.4187804317184434 chr7 159138663 13035550 0.08191315519598151 0.49970749617399374 chr8 146364022 18825092 0.12861830211252326 1.2749291948844184 chr9 141213431 11591257 0.08208324744974152 0.6319876327877608 chr10 135534747 9530521 0.07031791633476839 0.5992967561579019 chr11 135006516 15992978 0.11846078599643295 0.6453813495984706 chr12 133851895 7788184 0.058185085836849754 0.33057785172147924 chr13 115169878 9473146 0.08225367747632763 0.372815263363136 chr14 107349540 5905318 0.05501018448705043 0.35658973366225594 chr15 102531392 8372949 0.08166229714310326 0.374244214538169 chr16 90354753 6563517 0.0726416351334611 0.42062088100847445 chr17 81195210 4551783 0.056059747859510435 0.3492563922165269 chr18 78077248 6947218 0.08897877650605718 1.2384649338164684 chr19 59128983 3557980 0.06017319797298053 0.8918789408868222 chr20 63025520 6496808 0.10308218004389333 0.44693945527685164 chr21 48129895 2585490 0.05371900354239294 0.3607193295144856 chr22 51304566 2202164 0.04292335305984266 0.2606477987889987 chrMT 16571 275811 16.644197694767968 10.46535963956329 chrX 155270560 19723743 0.1270282209325451 0.5275790939336324 chrY 59373566 652513 0.010989958056418576 0.20822467189585334