BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006090.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 10,671,204 number of mapped reads = 9,287,839 (87.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,702,040 number of mapped paired reads (second in pair) = 4,585,799 number of mapped paired reads (both in pair) = 8,481,022 number of mapped paired reads (singletons) = 806,817 number of mapped bases = 357,891,191 bp number of sequenced bases = 357,853,914 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,157,459 duplication rate = 11.26% >>>>>>> Insert size mean insert size = 73,748.4397 std insert size = 2,680,864.7507 median insert size = 91 >>>>>>> Mapping quality mean mapping quality = 46.0988 >>>>>>> ACTG content number of A's = 92,900,626 bp (25.96%) number of C's = 81,353,764 bp (22.73%) number of T's = 96,526,795 bp (26.97%) number of G's = 87,058,302 bp (24.33%) number of N's = 14,427 bp (0%) GC percentage = 47.06% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,789,582 number of insertions = 12,474 mapped reads with insertion percentage = 0.13% number of deletions = 29,539 mapped reads with deletion percentage = 0.32% homopolymer indels = 43.56% >>>>>>> Coverage mean coverageData = 0.1156X std coverageData = 0.7547X There is a 4.61% of reference with a coverageData >= 1X There is a 2.64% of reference with a coverageData >= 2X There is a 1.59% of reference with a coverageData >= 3X There is a 0.99% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 30595843 0.12275132104886512 0.8316006720068533 chr2 243199373 31143744 0.12805848804552633 0.7761421850711965 chr3 198022430 23917832 0.12078344862246161 0.7022177156879277 chr4 191154276 20623992 0.10789186845080044 0.691156183516456 chr5 180915260 21492532 0.11879888960168423 0.6974511326182115 chr6 171115067 19858430 0.11605307672877223 0.7407574844948026 chr7 159138663 19634791 0.12338165113276087 0.8388473538318404 chr8 146364022 17760748 0.12134640574443903 0.8189317718585836 chr9 141213431 15425393 0.1092346024791367 0.6925963128282417 chr10 135534747 17423244 0.1285518613171573 0.7472117255710073 chr11 135006516 16612284 0.12304801643796215 1.1013474195050115 chr12 133851895 16546517 0.12361810043854814 0.7169827539106155 chr13 115169878 10529069 0.09142207305281681 0.6180372471600084 chr14 107349540 11005363 0.10251895816227997 0.662449877333801 chr15 102531392 10918491 0.10648924965341347 0.6691526117121618 chr16 90354753 12089508 0.13380046537230864 0.7784987855985687 chr17 81195210 11885246 0.14637865952929982 0.842635012136274 chr18 78077248 9205821 0.11790657631785383 0.761171237445886 chr19 59128983 9369779 0.15846338841985494 0.9468013812718034 chr20 63025520 8687374 0.13783898966640815 0.7754547297058109 chr21 48129895 4667967 0.09698685193474867 0.6810016174690254 chr22 51304566 5531547 0.10781783048315817 0.7175110354739802 chrMT 16571 24177 1.4589946291714442 2.480148408702668 chrX 155270560 10708521 0.06896684728901603 0.526122540178486 chrY 59373566 2232978 0.03760895884205439 0.3801902209628405