BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818847.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,761,509 number of mapped reads = 1,700,056 (96.51%) number of supplementary alignments = 28,138 (1.6%) number of secondary alignments = 0 number of mapped bases = 157,364,834 bp number of sequenced bases = 157,265,200 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 395,436 duplication rate = 20.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3662 >>>>>>> ACTG content number of A's = 45,701,164 bp (29.06%) number of C's = 33,072,451 bp (21.03%) number of T's = 45,524,638 bp (28.95%) number of G's = 32,964,583 bp (20.96%) number of N's = 2,364 bp (0%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 957,329 number of insertions = 21,455 mapped reads with insertion percentage = 1.22% number of deletions = 51,303 mapped reads with deletion percentage = 2.95% homopolymer indels = 40.64% >>>>>>> Coverage mean coverageData = 0.0508X std coverageData = 0.5756X There is a 3.47% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% 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% 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 14674658 0.05887511108748652 0.8507456266334169 chr2 243199373 11634768 0.04784045228603447 0.8388455259547261 chr3 198022430 9532651 0.048139248669961276 0.2989831781835123 chr4 191154276 9314413 0.048727201896336336 0.3805027019055866 chr5 180915260 8496636 0.046964728127411697 0.31078307783363307 chr6 171115067 7723124 0.0451340968121761 0.3142167986814741 chr7 159138663 13882170 0.08723316972947046 1.16739398569775 chr8 146364022 13278079 0.09071955538363109 0.5071577377185826 chr9 141213431 5700133 0.040365374310606474 0.46547054411309957 chr10 135534747 7167271 0.0528814282583934 0.7816860709414827 chr11 135006516 6774060 0.05017580040358941 0.36036145874206743 chr12 133851895 6937474 0.05182947914185301 0.3099105607070538 chr13 115169878 3873772 0.033635287865808106 0.24537090642737835 chr14 107349540 4544954 0.042337899165660144 0.3106639315989279 chr15 102531392 4290943 0.04185004140000362 0.2760753922728293 chr16 90354753 3857117 0.042688589940586746 0.6313954619469891 chr17 81195210 3801663 0.04682127184596234 0.37283656248642233 chr18 78077248 2767057 0.03543999143002581 0.5483822963200533 chr19 59128983 2557530 0.04325340755480269 0.7233491626258703 chr20 63025520 6195296 0.09829821316825312 0.4561562565018687 chr21 48129895 1907213 0.03962636943213776 0.31727474288153645 chr22 51304566 1370192 0.02670701863066145 0.24586387995720665 chrMT 16571 211987 12.792649809908877 8.328801501585538 chrX 155270560 6312280 0.04065342457707372 0.3247666464922183 chrY 59373566 559393 0.009421583335587423 0.6761103130807784