BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084273.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 = 1,631,608 number of mapped reads = 1,264,102 (77.48%) number of supplementary alignments = 9,632 (0.59%) number of secondary alignments = 0 number of mapped bases = 83,236,484 bp number of sequenced bases = 83,211,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,992 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0196 >>>>>>> ACTG content number of A's = 24,686,536 bp (29.67%) number of C's = 15,702,592 bp (18.87%) number of T's = 24,387,236 bp (29.31%) number of G's = 18,434,480 bp (22.15%) number of N's = 940 bp (0%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 679,602 number of insertions = 6,148 mapped reads with insertion percentage = 0.48% number of deletions = 15,377 mapped reads with deletion percentage = 1.2% homopolymer indels = 43.62% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.2614X There is a 2.52% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 6757529 0.027111382803736324 0.45184428815986044 chr2 243199373 7295971 0.029999958100220925 0.30786698311474225 chr3 198022430 5627672 0.02841936643237839 0.17606418849486474 chr4 191154276 5254497 0.027488252473096653 0.17672181292312078 chr5 180915260 5047307 0.027898735573770837 0.1746798107132129 chr6 171115067 4739591 0.0276982680899748 0.20538183101406227 chr7 159138663 4681973 0.029420713431531093 0.35756388251911597 chr8 146364022 4240541 0.028972564036262954 0.2458341651849515 chr9 141213431 3439347 0.024355664865900753 0.23778555736690127 chr10 135534747 4222370 0.031153413375243178 0.2864965935260631 chr11 135006516 3880966 0.028746508798138306 0.2306298702486172 chr12 133851895 3813562 0.02849090780522756 0.1776172528448283 chr13 115169878 2568833 0.022304729714135843 0.15483540041957963 chr14 107349540 2488813 0.02318419808785394 0.17456810524931496 chr15 102531392 2231827 0.02176725543724209 0.16088679163143763 chr16 90354753 2197868 0.02432487419892565 0.18508299280508123 chr17 81195210 2112668 0.026019613718592512 0.18780355157428083 chr18 78077248 2305067 0.029522902753949525 0.5071617505232142 chr19 59128983 1579421 0.02671145214860198 0.3420750010529524 chr20 63025520 1651519 0.02620397261299867 0.1743584136818881 chr21 48129895 1040744 0.021623649916543555 0.15816280050127457 chr22 51304566 830916 0.016195751465863682 0.13166990744678037 chrMT 16571 42378 2.557359242049363 2.1993316767765325 chrX 155270560 4983655 0.032096586757979106 0.20951454086562682 chrY 59373566 201449 0.003392907207224171 0.07783414435199862