BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716140.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 = 426,649 number of mapped reads = 384,430 (90.1%) number of supplementary alignments = 1,048 (0.25%) number of secondary alignments = 0 number of mapped bases = 22,231,080 bp number of sequenced bases = 22,224,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,955 duplication rate = 1.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0162 >>>>>>> ACTG content number of A's = 5,406,146 bp (24.33%) number of C's = 4,164,154 bp (18.74%) number of T's = 7,149,464 bp (32.17%) number of G's = 5,504,177 bp (24.77%) number of N's = 250 bp (0%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 108,970 number of insertions = 1,415 mapped reads with insertion percentage = 0.37% number of deletions = 4,208 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.13% >>>>>>> Coverage mean coverageData = 0.0072X std coverageData = 0.0977X There is a 0.69% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 2595360 0.010412652091245943 0.1261410741557245 chr2 243199373 2270655 0.009336598906445372 0.12023525635792759 chr3 198022430 1399927 0.007069537526632716 0.087001019186432 chr4 191154276 936440 0.00489887027167522 0.07309921176718129 chr5 180915260 1555752 0.008599340929007316 0.09549448393152998 chr6 171115067 866730 0.005065188093576821 0.07645278296761594 chr7 159138663 1507490 0.009472808000152672 0.13790898266437457 chr8 146364022 977192 0.006676449489752339 0.08942856099840923 chr9 141213431 602911 0.004269501815305373 0.07729750650630082 chr10 135534747 1045325 0.007712597862450726 0.10781171701150323 chr11 135006516 942612 0.006981974114493851 0.09667449019678966 chr12 133851895 891180 0.006657955795097261 0.08357911708954713 chr13 115169878 658886 0.005720992428245864 0.07762864781286043 chr14 107349540 455862 0.004246520292494966 0.06766491225012686 chr15 102531392 979178 0.009550031272373636 0.10038791554341923 chr16 90354753 665590 0.007366408272954938 0.09124692670386854 chr17 81195210 806188 0.00992900935904963 0.10452839290999398 chr18 78077248 714344 0.009149195422461611 0.13093628898791287 chr19 59128983 364958 0.00617223536552286 0.10072376999693285 chr20 63025520 588297 0.009334266500300196 0.09974132983096237 chr21 48129895 282197 0.005863237391230544 0.0790112173491744 chr22 51304566 250082 0.0048744589321737955 0.07153681884013365 chrMT 16571 5057 0.30517168547462437 0.5903574711585236 chrX 155270560 822273 0.005295743120911008 0.0802630812032362 chrY 59373566 46594 7.847600058248144E-4 0.031451867332732246