BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505953.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 = 6,833,191 number of mapped reads = 5,127,386 (75.04%) number of supplementary alignments = 244 (0%) number of secondary alignments = 0 number of mapped bases = 238,262,724 bp number of sequenced bases = 238,213,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 323,380 duplication rate = 4.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.278 >>>>>>> ACTG content number of A's = 70,366,915 bp (29.54%) number of C's = 49,253,568 bp (20.68%) number of T's = 69,201,760 bp (29.05%) number of G's = 49,390,841 bp (20.73%) number of N's = 695 bp (0%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,169,500 number of insertions = 10,090 mapped reads with insertion percentage = 0.2% number of deletions = 35,118 mapped reads with deletion percentage = 0.68% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.077X std coverageData = 0.6938X There is a 5.8% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 24431383 0.09801934655962201 1.535392122842133 chr2 243199373 15515266 0.06379648848847978 0.47604798866410025 chr3 198022430 16016652 0.0808830191610112 0.36328405247619194 chr4 191154276 10181739 0.053264510808013525 0.29558036116451497 chr5 180915260 14133620 0.07812287365919271 0.3564208131572945 chr6 171115067 17552866 0.10257931290176803 0.5491251854396917 chr7 159138663 16846949 0.10586333127607085 1.1921808436670978 chr8 146364022 15543452 0.10619721833006202 0.8762866802977541 chr9 141213431 6826392 0.04834095419719672 0.39270399194973743 chr10 135534747 8043934 0.05934960722655128 0.6827390821288247 chr11 135006516 12760262 0.09451589729194997 0.5759677439140879 chr12 133851895 7292237 0.05447989361674708 0.31283590486468266 chr13 115169878 7305366 0.06343122113926351 0.3145238269543178 chr14 107349540 9061445 0.08441065513648219 0.5170890189114289 chr15 102531392 4418214 0.043091329531544834 0.25633371337493843 chr16 90354753 8057076 0.08917157905351145 0.43608460984834246 chr17 81195210 3941964 0.04854921860538325 0.3154080772340229 chr18 78077248 6226353 0.07974606123412546 0.699457526550685 chr19 59128983 6207141 0.10497628548760934 1.1841513099800793 chr20 63025520 5684403 0.09019208409545848 0.3920270310445899 chr21 48129895 3751873 0.07795306846191956 0.3770112500235476 chr22 51304566 1677390 0.03269475079469535 0.22354742937467847 chrMT 16571 31107 1.8771950998732725 1.9376965298857252 chrX 155270560 16051068 0.10337483164870405 0.45894243824365205 chrY 59373566 704572 0.011866762390522409 0.16642387176017617