BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818828.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 = 2,284,291 number of mapped reads = 2,229,905 (97.62%) number of supplementary alignments = 16,699 (0.73%) number of secondary alignments = 0 number of mapped bases = 151,703,250 bp number of sequenced bases = 151,640,694 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,087,873 duplication rate = 40.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7728 >>>>>>> ACTG content number of A's = 42,486,328 bp (28.02%) number of C's = 32,158,201 bp (21.21%) number of T's = 43,794,079 bp (28.88%) number of G's = 33,193,002 bp (21.89%) number of N's = 9,084 bp (0.01%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 753,855 number of insertions = 19,124 mapped reads with insertion percentage = 0.85% number of deletions = 37,772 mapped reads with deletion percentage = 1.68% homopolymer indels = 38.99% >>>>>>> Coverage mean coverageData = 0.049X std coverageData = 0.6045X There is a 2.12% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 13192119 0.05292712590673947 0.89227458801385 chr2 243199373 13142929 0.05404178817516935 0.9934970465430298 chr3 198022430 10134869 0.05118040920919918 0.44255530547221056 chr4 191154276 9511688 0.049759221708438266 0.49637852219925943 chr5 180915260 8992480 0.04970548089752075 0.4452333337693033 chr6 171115067 8771537 0.05126104412535455 0.4832469206727168 chr7 159138663 7987520 0.05019220250706769 0.514365225738256 chr8 146364022 7640674 0.05220322518876941 0.49664649808523575 chr9 141213431 6536992 0.04629157406422623 0.5054119722086645 chr10 135534747 7299575 0.053857591219763 0.6505521855145455 chr11 135006516 7217570 0.05346090110198829 0.510982779048604 chr12 133851895 7143283 0.0533670666373457 0.47902326496699876 chr13 115169878 4630917 0.04020944608450484 0.39571703637784456 chr14 107349540 4773856 0.04447020452998681 0.4520851472385021 chr15 102531392 4592401 0.04479019459718249 0.4179974643438225 chr16 90354753 4914466 0.05439078561810689 0.6971040269810035 chr17 81195210 4490023 0.05529911185647528 0.49171651189991883 chr18 78077248 3843600 0.0492281695174502 0.6372674132704398 chr19 59128983 3333083 0.05636969944164269 0.769646975290609 chr20 63025520 3554242 0.05639369576006672 0.5142874663906476 chr21 48129895 1999588 0.04154565473288483 0.4229222846465335 chr22 51304566 1971879 0.03843476621554503 0.41701520067025993 chrMT 16571 131906 7.9600506909661455 7.999708962950332 chrX 155270560 4556507 0.029345595198471623 0.3839959899601134 chrY 59373566 1339546 0.022561319628334266 0.8795285064567431