BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084407.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 = 2,469,330 number of mapped reads = 1,382,518 (55.99%) number of supplementary alignments = 6,809 (0.28%) number of secondary alignments = 0 number of mapped bases = 88,755,877 bp number of sequenced bases = 88,727,461 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,213 duplication rate = 2.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7333 >>>>>>> ACTG content number of A's = 25,436,715 bp (28.67%) number of C's = 16,499,980 bp (18.6%) number of T's = 26,835,980 bp (30.25%) number of G's = 19,953,788 bp (22.49%) number of N's = 998 bp (0%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 755,626 number of insertions = 6,455 mapped reads with insertion percentage = 0.46% number of deletions = 18,229 mapped reads with deletion percentage = 1.31% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2241X There is a 2.6% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.02% 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 6841726 0.0274491833663275 0.2960224454683203 chr2 243199373 7519299 0.030918249941376288 0.27851036936183543 chr3 198022430 6363998 0.03213776338367325 0.1937045822082311 chr4 191154276 6006299 0.03142121183833732 0.19483281952323575 chr5 180915260 5412060 0.029914889434976354 0.1864008364163569 chr6 171115067 5258552 0.0307310869357869 0.21093467629192772 chr7 159138663 4912681 0.030870442841410575 0.24660258187637832 chr8 146364022 4489654 0.030674573837551417 0.23321899668793086 chr9 141213431 3596609 0.025469312476374857 0.21122366179234361 chr10 135534747 4116271 0.030370595667249815 0.233820586665157 chr11 135006516 4061016 0.03008014813151685 0.210988822292835 chr12 133851895 4186997 0.03128081974483813 0.1913990761295948 chr13 115169878 2763977 0.023999131092246186 0.16838045716449263 chr14 107349540 2683770 0.025000293433954164 0.17618847068022658 chr15 102531392 2420283 0.023605287637175548 0.16908062267366863 chr16 90354753 2489663 0.027554311393004415 0.1929980531481202 chr17 81195210 2184698 0.02690673501552616 0.1877667573757217 chr18 78077248 2346855 0.030058116290164326 0.38684249106875973 chr19 59128983 1661699 0.028102952489475422 0.26396563521252064 chr20 63025520 1868402 0.029645165958170596 0.1903962332944184 chr21 48129895 1101422 0.02288436324242968 0.16931696985997655 chr22 51304566 885445 0.017258600335884333 0.14107797382626602 chrMT 16571 43851 2.6462494719691025 2.1513152107610405 chrX 155270560 5336779 0.03437083630019754 0.21424500054033024 chrY 59373566 203871 0.003433699771376373 0.07620431352237016