BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080796.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 = 2,565,970 number of mapped reads = 2,353,265 (91.71%) number of supplementary alignments = 18,070 (0.7%) number of secondary alignments = 0 number of mapped bases = 160,594,083 bp number of sequenced bases = 160,535,890 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,642 duplication rate = 5.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1493 >>>>>>> ACTG content number of A's = 45,633,877 bp (28.43%) number of C's = 29,760,809 bp (18.54%) number of T's = 50,953,983 bp (31.74%) number of G's = 34,164,220 bp (21.28%) number of N's = 23,001 bp (0.01%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,267,776 number of insertions = 11,973 mapped reads with insertion percentage = 0.5% number of deletions = 32,934 mapped reads with deletion percentage = 1.39% homopolymer indels = 48.72% >>>>>>> Coverage mean coverageData = 0.0519X std coverageData = 0.3682X There is a 3.88% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 12848209 0.05154735000640179 0.5540021210560941 chr2 243199373 13806263 0.05676931987813965 0.42193060359241946 chr3 198022430 11480208 0.05797428099432978 0.3064232174995164 chr4 191154276 10733132 0.05614905522699372 0.3094071819115733 chr5 180915260 10306926 0.05697101504870291 0.30318157746248253 chr6 171115067 9727978 0.056850505163288746 0.3410235423026529 chr7 159138663 8336903 0.05238766521495785 0.3517753178284335 chr8 146364022 8055589 0.05503804070101326 0.5667968629124133 chr9 141213431 6667344 0.04721465906454748 0.32805048601902637 chr10 135534747 7049009 0.05200886972548818 0.34571690759454515 chr11 135006516 6979247 0.05169563075014839 0.3070189955897314 chr12 133851895 7274953 0.054350765822179806 0.2985694445687032 chr13 115169878 5239803 0.04549629721757628 0.2722505428526149 chr14 107349540 5058896 0.04712545577745373 0.2886553945736541 chr15 102531392 5215132 0.05086375887689109 0.2874359464178567 chr16 90354753 4240121 0.04692748150172023 0.2957213455228182 chr17 81195210 3970298 0.04889818007737156 0.29680754795694547 chr18 78077248 4615677 0.05911679930112291 0.5449779573625957 chr19 59128983 2606009 0.044073293125978505 0.4216274572304555 chr20 63025520 3516106 0.055788607535487214 0.3052859053244956 chr21 48129895 2157054 0.044817342734697424 0.28330970388273724 chr22 51304566 1635073 0.031869931420918755 0.2256257316048209 chrMT 16571 64038 3.864462011948585 2.9410387715922566 chrX 155270560 8622188 0.05553008889772794 0.30701787527482705 chrY 59373566 387927 0.006533665166751143 0.15513862399178868