BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230400.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 = 294,171 number of mapped reads = 265,996 (90.42%) number of supplementary alignments = 1,958 (0.67%) number of secondary alignments = 0 number of mapped bases = 18,050,141 bp number of sequenced bases = 18,041,459 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,397 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4647 >>>>>>> ACTG content number of A's = 5,273,443 bp (29.23%) number of C's = 3,305,230 bp (18.32%) number of T's = 5,735,112 bp (31.79%) number of G's = 3,717,367 bp (20.6%) number of N's = 10,307 bp (0.06%) GC percentage = 38.92% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 161,262 number of insertions = 1,514 mapped reads with insertion percentage = 0.56% number of deletions = 5,155 mapped reads with deletion percentage = 1.92% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 0.0058X std coverageData = 0.0907X There is a 0.55% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 1474205 0.005914548955125773 0.11932042241861 chr2 243199373 1889537 0.007769497826789216 0.09908826262740845 chr3 198022430 1104567 0.005577989321714717 0.07754032871870241 chr4 191154276 1214929 0.0063557511002265 0.0835869399500415 chr5 180915260 1056580 0.00584019280628953 0.07912884344709106 chr6 171115067 1078312 0.006301677689200799 0.08485393630508012 chr7 159138663 1092616 0.006865811107134914 0.1067682809039796 chr8 146364022 1084150 0.007407216508439485 0.13075044325825805 chr9 141213431 755168 0.005347706621475687 0.08678696510932446 chr10 135534747 877968 0.006477807495372386 0.0964474554773259 chr11 135006516 735024 0.0054443594411398635 0.08307839815577224 chr12 133851895 847297 0.006330108363426607 0.0825952261619796 chr13 115169878 544179 0.0047250115173344195 0.07086490468400193 chr14 107349540 575448 0.005360507366869015 0.07672904243049158 chr15 102531392 473072 0.004613923509397005 0.06991729678363973 chr16 90354753 437169 0.004838361961987767 0.07406444970412669 chr17 81195210 345079 0.004249992086971633 0.06872140048934361 chr18 78077248 451949 0.005788485270382481 0.12238258780963625 chr19 59128983 256488 0.004337771207734116 0.08781117236470737 chr20 63025520 280117 0.004444501211572709 0.0692220966098148 chr21 48129895 268305 0.005574601814527125 0.07885159422441135 chr22 51304566 141173 0.002751665417070286 0.053924470791935325 chrMT 16571 1830 0.11043389053165167 0.3467049634537814 chrX 155270560 1021621 0.006579618183897836 0.08522935457617245 chrY 59373566 43358 7.302576368749689E-4 0.031740751938082394