BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505986.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 8,997,537 number of mapped reads = 6,471,322 (71.92%) number of supplementary alignments = 237 (0%) number of secondary alignments = 0 number of mapped bases = 302,176,669 bp number of sequenced bases = 302,119,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 417,453 duplication rate = 4.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0753 >>>>>>> ACTG content number of A's = 92,679,854 bp (30.68%) number of C's = 58,932,162 bp (19.51%) number of T's = 90,634,157 bp (30%) number of G's = 59,872,125 bp (19.82%) number of N's = 1,204 bp (0%) GC percentage = 39.32% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,403,874 number of insertions = 14,293 mapped reads with insertion percentage = 0.22% number of deletions = 42,167 mapped reads with deletion percentage = 0.65% homopolymer indels = 47.55% >>>>>>> Coverage mean coverageData = 0.0976X std coverageData = 1.0154X There is a 6.4% of reference with a coverageData >= 1X There is a 2.06% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23807686 0.09551705790935622 2.184393667502667 chr2 243199373 26566760 0.10923860399919699 0.7347190476414042 chr3 198022430 20639416 0.10422766754251021 0.4707219261616863 chr4 191154276 20286334 0.10612545230220223 0.47373470286215297 chr5 180915260 19257636 0.10644561437216518 0.47654701329243254 chr6 171115067 17618647 0.10296373842988356 0.536043977977747 chr7 159138663 17080169 0.10732884566210035 1.1505965392762432 chr8 146364022 16124401 0.11016642464225258 2.094723868006256 chr9 141213431 12192746 0.08634267940136657 0.6664266332289959 chr10 135534747 13902369 0.10257420556516035 0.9210954915055743 chr11 135006516 13600308 0.10073815992703641 0.7407120852974673 chr12 133851895 12888026 0.09628571937662893 0.49083536087885593 chr13 115169878 10688967 0.0928104395491328 0.42474495125446093 chr14 107349540 9665161 0.09003448920228256 0.6533890523494329 chr15 102531392 7827833 0.07634572053795972 0.38220550481802407 chr16 90354753 8189862 0.09064118630261764 0.5099021100472597 chr17 81195210 6695133 0.08245724101212375 0.4856856929646096 chr18 78077248 8109838 0.10386941404492125 1.6428475922970125 chr19 59128983 5281343 0.08931902312610383 1.4727870127885456 chr20 63025520 5663080 0.08985376082577343 0.4331381882468505 chr21 48129895 4165256 0.08654197147116154 0.4630925316101161 chr22 51304566 3029962 0.059058330207880524 0.32594700562169 chrMT 16571 39731 2.3976223523022147 2.5592567736052234 chrX 155270560 17995259 0.11589614283609205 0.6339429889874858 chrY 59373566 860746 0.014497124865297799 0.21512598360742788