BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085114.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 = 1,192,137 number of mapped reads = 988,428 (82.91%) number of supplementary alignments = 7,748 (0.65%) number of secondary alignments = 0 number of mapped bases = 63,182,661 bp number of sequenced bases = 63,159,932 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,412 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0017 >>>>>>> ACTG content number of A's = 18,839,937 bp (29.83%) number of C's = 12,118,071 bp (19.19%) number of T's = 18,334,631 bp (29.03%) number of G's = 13,866,016 bp (21.95%) number of N's = 1,277 bp (0%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 575,602 number of insertions = 4,978 mapped reads with insertion percentage = 0.5% number of deletions = 14,032 mapped reads with deletion percentage = 1.4% homopolymer indels = 45.18% >>>>>>> Coverage mean coverageData = 0.0204X std coverageData = 0.1818X There is a 1.92% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 7278923 0.029203229146618655 0.2743149715043136 chr2 243199373 6070038 0.024959102176632667 0.20028973185577156 chr3 198022430 4046813 0.020436134431841887 0.1502128284796829 chr4 191154276 3453137 0.018064659981762585 0.14006078337734043 chr5 180915260 3091589 0.017088602697196465 0.13578442974625063 chr6 171115067 3871085 0.022622701015568663 0.16892065368181267 chr7 159138663 5219890 0.032800891383635664 0.21031196590392162 chr8 146364022 3597012 0.024575793633219507 0.2924855195418014 chr9 141213431 1514966 0.010728200492487149 0.13549029617832936 chr10 135534747 3811843 0.028124470546287292 0.22350071663251952 chr11 135006516 3475606 0.025743987053187863 0.19395223490415664 chr12 133851895 2887094 0.02156931734137944 0.15626161709051817 chr13 115169878 1141572 0.009912070932297071 0.10288818915009221 chr14 107349540 2236793 0.020836540147260996 0.15162101164562253 chr15 102531392 1181410 0.011522422323106664 0.11107735318629391 chr16 90354753 1737023 0.019224478428932233 0.14818412138181905 chr17 81195210 1161611 0.014306398123731683 0.13168615320632862 chr18 78077248 1599807 0.020490053645333402 0.22430710244000737 chr19 59128983 886626 0.014994778449005288 0.1835068291660504 chr20 63025520 1504768 0.023875534862703236 0.16179999314972274 chr21 48129895 975285 0.02026360123993622 0.14951500947851798 chr22 51304566 445020 0.008674081757167579 0.09616337626941236 chrMT 16571 5271 0.31808581256411805 0.6335807194089309 chrX 155270560 1889612 0.012169802182718991 0.12346556366059681 chrY 59373566 99867 0.001682011149540858 0.046687929535334155