BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708600.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,712,385 number of mapped reads = 4,600,302 (97.62%) number of supplementary alignments = 133 (0%) number of secondary alignments = 0 number of mapped bases = 229,454,854 bp number of sequenced bases = 229,435,435 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,712 duplication rate = 0.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7792 >>>>>>> ACTG content number of A's = 71,084,060 bp (30.98%) number of C's = 43,470,982 bp (18.95%) number of T's = 70,865,907 bp (30.89%) number of G's = 44,006,250 bp (19.18%) number of N's = 8,236 bp (0%) GC percentage = 38.13% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 332,167 number of insertions = 14,382 mapped reads with insertion percentage = 0.31% number of deletions = 11,345 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.0741X std coverageData = 0.2831X There is a 6.88% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0% 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 17691441 0.0709785232591256 0.2784680664311569 chr2 243199373 20394286 0.08385830007875884 0.29980174395685305 chr3 198022430 17628008 0.08902025896763312 0.30885497441162174 chr4 191154276 17688106 0.09253314322929401 0.31414592771805566 chr5 180915260 16024368 0.0885738881286189 0.30811880727972485 chr6 171115067 15297659 0.08939983642702837 0.30951948845506083 chr7 159138663 12602795 0.07919379717297235 0.29212639166786464 chr8 146364022 12299716 0.08403510529384059 0.2998897974872615 chr9 141213431 9798896 0.06939067998425731 0.27442203093587697 chr10 135534747 9953730 0.0734404292649766 0.2803910549653256 chr11 135006516 10664902 0.07899546122647888 0.2929333675675929 chr12 133851895 11008873 0.08224667271240352 0.2979532489368048 chr13 115169878 8598664 0.07466070251459327 0.2839676415826003 chr14 107349540 7149891 0.06660383453902084 0.2696871151925287 chr15 102531392 6002781 0.05854578664064173 0.25281964774022375 chr16 90354753 4271682 0.047276782439989624 0.22585074969221897 chr17 81195210 3900688 0.04804086349428741 0.228968088947627 chr18 78077248 6334163 0.0811268732217611 0.29491821522264117 chr19 59128983 1880431 0.03180218743150039 0.1838428295775819 chr20 63025520 3442443 0.054619827016103954 0.24190160630094057 chr21 48129895 2660339 0.05527414925796119 0.2459655616055876 chr22 51304566 1268824 0.024731210083718473 0.16290664583399084 chrMT 16571 259 0.01562971456158349 0.12403800459660302 chrX 155270560 12592209 0.08109849671438037 0.29520855739049867 chrY 59373566 299700 0.005047700857314179 0.07403153801252377