BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063568.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 = 2,600,928 number of mapped reads = 2,319,585 (89.18%) number of supplementary alignments = 18,556 (0.71%) number of secondary alignments = 0 number of mapped bases = 151,623,176 bp number of sequenced bases = 151,557,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,084 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3423 >>>>>>> ACTG content number of A's = 42,354,332 bp (27.95%) number of C's = 27,789,667 bp (18.34%) number of T's = 48,070,328 bp (31.72%) number of G's = 33,339,714 bp (22%) number of N's = 3,067 bp (0%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,186,068 number of insertions = 11,133 mapped reads with insertion percentage = 0.48% number of deletions = 40,688 mapped reads with deletion percentage = 1.74% homopolymer indels = 46.22% >>>>>>> Coverage mean coverageData = 0.049X std coverageData = 0.4791X There is a 3.99% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 19006717 0.0762554449162235 1.0166160347557163 chr2 243199373 16606496 0.06828346551699374 0.5115110880924795 chr3 198022430 12340195 0.06231715770784148 0.301439520099499 chr4 191154276 10824086 0.0566248698511981 0.28116517775146055 chr5 180915260 4318797 0.023871933191263135 0.18293420433707078 chr6 171115067 16692896 0.09755363038837486 0.470420380980707 chr7 159138663 14008103 0.08802451105172349 0.7610604632465691 chr8 146364022 5767752 0.03940689741362806 0.6805665094072517 chr9 141213431 1786851 0.012653548514092828 0.2615235352055913 chr10 135534747 6650935 0.049071807394158486 0.4723077800936972 chr11 135006516 2069329 0.015327623149685604 0.1865327431244014 chr12 133851895 5031095 0.03758702855869168 0.23389055903298184 chr13 115169878 897676 0.0077943644257398624 0.10653854464877202 chr14 107349540 1932355 0.018000589476210145 0.1813651584939373 chr15 102531392 4768328 0.04650603007515981 0.26051147307455763 chr16 90354753 2600473 0.02878069956098491 0.21753340599418447 chr17 81195210 3942387 0.04855442827230818 0.26995144196224996 chr18 78077248 3722443 0.04767641144319021 0.5846862583833934 chr19 59128983 2390808 0.04043377509131182 0.6225454468149454 chr20 63025520 1583223 0.025120348074875065 0.20330386455905075 chr21 48129895 2956822 0.06143420840623068 0.29555485976741164 chr22 51304566 1792705 0.03494240649068155 0.21738767925672986 chrMT 16571 42327 2.5542815762476616 2.373900999806799 chrX 155270560 9537559 0.06142541767093517 0.327323363761113 chrY 59373566 352818 0.005942341411664578 0.108539891775189