BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083660.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,418,047 number of mapped reads = 1,974,323 (81.65%) number of supplementary alignments = 13,537 (0.56%) number of secondary alignments = 0 number of mapped bases = 116,290,321 bp number of sequenced bases = 116,256,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,728 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9241 >>>>>>> ACTG content number of A's = 35,013,647 bp (30.12%) number of C's = 23,255,879 bp (20%) number of T's = 33,579,562 bp (28.88%) number of G's = 24,400,289 bp (20.99%) number of N's = 6,689 bp (0.01%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 934,508 number of insertions = 7,945 mapped reads with insertion percentage = 0.4% number of deletions = 21,801 mapped reads with deletion percentage = 1.1% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.2969X There is a 3.33% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 12525076 0.05025093197260279 0.573563410067236 chr2 243199373 9776851 0.040200971241813196 0.28652843687621526 chr3 198022430 9978498 0.050390746139212614 0.24833346172578133 chr4 191154276 5695440 0.029794991350337356 0.19029813775175394 chr5 180915260 5730737 0.03167636052370596 0.19520164465969286 chr6 171115067 7420205 0.04336383189447601 0.25924493668977894 chr7 159138663 8820602 0.05542714657593925 0.46280269861383333 chr8 146364022 7272678 0.049688973428183056 0.3766680062830479 chr9 141213431 4566899 0.032340401105331124 0.23733191116904043 chr10 135534747 4775115 0.035231666459671775 0.24594307521938416 chr11 135006516 4261636 0.03156615048121085 0.2101888446141104 chr12 133851895 3908857 0.029202851405278948 0.1886039324289155 chr13 115169878 3652749 0.031716183636141385 0.19432214132601747 chr14 107349540 2563430 0.023879282575407404 0.171089387046273 chr15 102531392 2912149 0.028402511106062032 0.18512503549132148 chr16 90354753 2856092 0.03160975936705842 0.20213348248492474 chr17 81195210 2297334 0.028293959705258474 0.18977618807941363 chr18 78077248 4144117 0.05307713970656343 0.37079839842955037 chr19 59128983 2664802 0.045067610921026666 0.40245987404144706 chr20 63025520 2438554 0.038691533207500704 0.21952032606125474 chr21 48129895 1820861 0.03783222464956552 0.21550250032467447 chr22 51304566 794362 0.015483261275419423 0.13380831871984086 chrMT 16571 14237 0.8591515297809426 1.049573717866394 chrX 155270560 5163827 0.03325696126812449 0.20880861004228224 chrY 59373566 235213 0.003961577783621755 0.08117024990402133