BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089707.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 20,714,027 number of mapped reads = 19,357,478 (93.45%) number of supplementary alignments = 152,149 (0.73%) number of secondary alignments = 0 number of mapped bases = 1,257,916,818 bp number of sequenced bases = 1,257,459,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,897,992 duplication rate = 17.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9912 >>>>>>> ACTG content number of A's = 326,733,818 bp (25.98%) number of C's = 229,318,586 bp (18.24%) number of T's = 399,507,493 bp (31.77%) number of G's = 301,839,820 bp (24%) number of N's = 59,313 bp (0%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 7,520,952 number of insertions = 82,563 mapped reads with insertion percentage = 0.42% number of deletions = 260,704 mapped reads with deletion percentage = 1.33% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 0.4063X std coverageData = 2.6465X There is a 12.01% of reference with a coverageData >= 1X There is a 7.59% of reference with a coverageData >= 2X There is a 5.25% of reference with a coverageData >= 3X There is a 3.74% of reference with a coverageData >= 4X There is a 2.7% of reference with a coverageData >= 5X There is a 1.98% of reference with a coverageData >= 6X There is a 1.47% of reference with a coverageData >= 7X There is a 1.1% of reference with a coverageData >= 8X There is a 0.84% of reference with a coverageData >= 9X There is a 0.64% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.39% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 105984497 0.4252125694804187 4.467509909582749 chr2 243199373 105224337 0.4326669748445445 3.2194139423805073 chr3 198022430 81966929 0.41392749801121015 1.6589279244212995 chr4 191154276 80928559 0.42336776709091245 1.9576798015062704 chr5 180915260 81163128 0.4486251076885388 1.7232626687232102 chr6 171115067 74860942 0.43748889745635317 2.4117638174251854 chr7 159138663 67740540 0.42566990775836794 2.640326697764811 chr8 146364022 63308999 0.4325448162390618 3.693749002148972 chr9 141213431 51781906 0.36669249966740064 2.481072829439562 chr10 135534747 61127133 0.4510070985708189 2.843042228364187 chr11 135006516 57493252 0.4258553861207706 2.417107740623242 chr12 133851895 57592221 0.4302682528327298 2.019939598088097 chr13 115169878 38498872 0.3342790030566847 1.4744836915218835 chr14 107349540 38184491 0.3557024184733349 1.603698148196996 chr15 102531392 35828749 0.34944174950828716 1.9553792263916245 chr16 90354753 35014715 0.387524882061268 1.8912316686385187 chr17 81195210 34337285 0.4228979147907863 2.022952021039488 chr18 78077248 33436894 0.42825400300994215 4.71400366666006 chr19 59128983 24197394 0.40923068133947105 2.8260092256940643 chr20 63025520 25851276 0.4101715622497046 1.8569129773251223 chr21 48129895 16082219 0.33414199220671476 1.8840344095590011 chr22 51304566 14003118 0.27294096981543514 1.3557689802388615 chrMT 16571 239741 14.467503469917325 11.19768518331575 chrX 155270560 69708783 0.4489504191908627 1.9258704724419078 chrY 59373566 3360838 0.056604954467447684 1.3832838132816