BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084903.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 = 2,436,641 number of mapped reads = 2,190,293 (89.89%) number of supplementary alignments = 16,751 (0.69%) number of secondary alignments = 0 number of mapped bases = 149,448,369 bp number of sequenced bases = 149,392,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,512 duplication rate = 4.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3966 >>>>>>> ACTG content number of A's = 42,854,844 bp (28.69%) number of C's = 27,030,544 bp (18.09%) number of T's = 48,163,908 bp (32.24%) number of G's = 31,319,700 bp (20.96%) number of N's = 23,107 bp (0.02%) GC percentage = 39.06% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,214,600 number of insertions = 11,339 mapped reads with insertion percentage = 0.51% number of deletions = 32,403 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.73% >>>>>>> Coverage mean coverageData = 0.0483X std coverageData = 0.3452X There is a 4.03% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12148313 0.04873934897839231 0.5034483170354541 chr2 243199373 13923253 0.0572503655262302 0.4055071353305066 chr3 198022430 11724203 0.05920643939173961 0.28086926038802906 chr4 191154276 9438576 0.049376745304928464 0.2577815547254395 chr5 180915260 7732619 0.04274166258833003 0.24004520297957094 chr6 171115067 8876403 0.0518738832039846 0.2723063341391792 chr7 159138663 8793893 0.05525931181161174 0.3700722699883228 chr8 146364022 9273291 0.06335772188605203 0.5808824815733238 chr9 141213431 9814759 0.06950301349168408 0.38771995176807617 chr10 135534747 4718967 0.03481739630944971 0.2632038424104689 chr11 135006516 6242593 0.046239197817681627 0.29579137568487757 chr12 133851895 6380689 0.04766976963605932 0.2523343204312839 chr13 115169878 3462567 0.030064866440164154 0.1983411554769913 chr14 107349540 3029086 0.02821703753923864 0.19815828596060017 chr15 102531392 3711334 0.03619705075300255 0.2183195206545491 chr16 90354753 2709179 0.02998380173757987 0.21429757689081855 chr17 81195210 2909170 0.035829330326259394 0.2291767552008303 chr18 78077248 5658342 0.0724710737755511 0.608893495697057 chr19 59128983 2733024 0.04622139366070274 0.3426294097104725 chr20 63025520 3000827 0.047612887604894016 0.25560784390328284 chr21 48129895 1403095 0.029152255578367665 0.20739346397561667 chr22 51304566 1299363 0.025326459247311438 0.18067172758657526 chrMT 16571 360813 21.773761390380784 11.063132492926815 chrX 155270560 9775277 0.06295640976628152 0.3100803119148971 chrY 59373566 328733 0.0055366895092674746 0.13405997144063378