BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708565.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 = 4,187,669 number of mapped reads = 3,430,974 (81.93%) number of supplementary alignments = 94 (0%) number of secondary alignments = 0 number of mapped bases = 171,096,662 bp number of sequenced bases = 171,081,699 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,358 duplication rate = 0.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5322 >>>>>>> ACTG content number of A's = 52,992,819 bp (30.98%) number of C's = 32,498,850 bp (19%) number of T's = 52,758,733 bp (30.84%) number of G's = 32,826,516 bp (19.19%) number of N's = 4,781 bp (0%) GC percentage = 38.18% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 272,093 number of insertions = 11,829 mapped reads with insertion percentage = 0.34% number of deletions = 9,038 mapped reads with deletion percentage = 0.26% homopolymer indels = 47.47% >>>>>>> Coverage mean coverageData = 0.0553X std coverageData = 0.2417X There is a 5.24% of reference with a coverageData >= 1X There is a 0.27% 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 13160003 0.052798275676111554 0.23726985261681527 chr2 243199373 15032790 0.061812618242235357 0.2549266867199109 chr3 198022430 13056055 0.06593220273077145 0.2629579191023157 chr4 191154276 13705349 0.07169784159052764 0.2740146807359194 chr5 180915260 11703410 0.06469001011854943 0.26015770434260355 chr6 171115067 11418481 0.06672983975163332 0.26474905808359617 chr7 159138663 9401575 0.059077881030080034 0.24957415889694168 chr8 146364022 9186870 0.06276726940449888 0.25644855256074806 chr9 141213431 7117449 0.05040206834150216 0.23107974800086714 chr10 135534747 6877261 0.05074168176224212 0.23048665689969897 chr11 135006516 7770992 0.05756012546831443 0.24713254397980494 chr12 133851895 7902813 0.05904147266648709 0.24942957641730115 chr13 115169878 6340468 0.05505317979063935 0.24111132024736448 chr14 107349540 5421693 0.050505041754254375 0.23159405973856842 chr15 102531392 4667269 0.04552039047709408 0.2202643912499693 chr16 90354753 3236052 0.035814961499590396 0.194345573447182 chr17 81195210 2803867 0.03453241884589005 0.19126952284616905 chr18 78077248 4647606 0.059525740456425925 0.24928063867719824 chr19 59128983 1436945 0.024301872399868606 0.1591989789919116 chr20 63025520 2570632 0.040787160502602754 0.20711418381797184 chr21 48129895 2024437 0.04206194507592423 0.21260555991753693 chr22 51304566 962052 0.018751781274204717 0.14026361671898996 chrMT 16571 200 0.012069277653732424 0.10919528465391506 chrX 155270560 10413333 0.06706572707665896 0.26586988517846094 chrY 59373566 239060 0.004026370927425852 0.06583489986890712