BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524503.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 565,328 number of mapped reads = 504,155 (89.18%) number of supplementary alignments = 1,711 (0.3%) number of secondary alignments = 0 number of mapped bases = 28,340,200 bp number of sequenced bases = 28,326,494 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,020 duplication rate = 5.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5319 >>>>>>> ACTG content number of A's = 6,723,094 bp (23.73%) number of C's = 5,183,011 bp (18.3%) number of T's = 9,246,248 bp (32.64%) number of G's = 7,173,604 bp (25.32%) number of N's = 537 bp (0%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 160,669 number of insertions = 1,784 mapped reads with insertion percentage = 0.35% number of deletions = 8,105 mapped reads with deletion percentage = 1.59% homopolymer indels = 41.72% >>>>>>> Coverage mean coverageData = 0.0092X std coverageData = 0.1289X There is a 0.77% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 2804971 0.011253616896705745 0.17979437169640589 chr2 243199373 2176907 0.008951120938950776 0.15230292813850727 chr3 198022430 1510399 0.007627413722778778 0.10096895338650622 chr4 191154276 1605257 0.008397703852567755 0.11832672776483426 chr5 180915260 1587596 0.008775357037322335 0.10788928444040592 chr6 171115067 1190347 0.0069564125524960345 0.10335002561874743 chr7 159138663 1433558 0.009008232022157935 0.14835895469778992 chr8 146364022 2588127 0.017682808689146297 0.1641338664063236 chr9 141213431 1173848 0.008312580408870599 0.11534336902647754 chr10 135534747 1489600 0.010990539569900846 0.15065722358883174 chr11 135006516 980292 0.007261071754492206 0.11425444004400831 chr12 133851895 1289067 0.009630547255233107 0.11381745423788386 chr13 115169878 629130 0.005462626260661663 0.08472590640330861 chr14 107349540 678090 0.006316654919993136 0.09208902564719537 chr15 102531392 777766 0.007585637772283439 0.10155525125124922 chr16 90354753 888462 0.009833041101888686 0.11780213858774505 chr17 81195210 1014909 0.012499616664579105 0.13301468724082555 chr18 78077248 659253 0.008443599344075242 0.1488033589179169 chr19 59128983 619093 0.010470212213864731 0.13845517364699633 chr20 63025520 812221 0.012887176496124109 0.13398394031629604 chr21 48129895 395054 0.008208079406780339 0.11174850993250242 chr22 51304566 241219 0.004701706276981273 0.07951437760548512 chrMT 16571 6800 0.4103554402269024 0.7588801793960774 chrX 155270560 1667940 0.010742152279221508 0.12307214060022777 chrY 59373566 120294 0.0020260531429087485 0.08150304864467552