BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525060.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 = 2,463,152 number of mapped reads = 2,263,848 (91.91%) number of supplementary alignments = 6,812 (0.28%) number of secondary alignments = 0 number of mapped bases = 132,621,790 bp number of sequenced bases = 132,581,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 235,360 duplication rate = 8.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3177 >>>>>>> ACTG content number of A's = 33,276,039 bp (25.1%) number of C's = 23,496,756 bp (17.72%) number of T's = 41,827,574 bp (31.55%) number of G's = 33,968,425 bp (25.62%) number of N's = 13,081 bp (0.01%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 637,131 number of insertions = 9,270 mapped reads with insertion percentage = 0.41% number of deletions = 24,947 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.0428X std coverageData = 0.4095X There is a 3.36% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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% 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 9236397 0.03705666594908905 0.7999464231516368 chr2 243199373 11762446 0.048365445415848175 0.4952207653566013 chr3 198022430 7175662 0.036236612185801376 0.23453300552771109 chr4 191154276 8922886 0.04667897672349218 0.3251049962708257 chr5 180915260 8272658 0.04572670099802526 0.2625967609674605 chr6 171115067 7700345 0.045000975863802806 0.28743974984348264 chr7 159138663 7493731 0.04708931732070666 0.464624348411895 chr8 146364022 6935711 0.04738672048790788 0.47272267188089684 chr9 141213431 5735070 0.040612779955753645 0.3206228307896308 chr10 135534747 6471270 0.047746206365811124 0.44808788405409694 chr11 135006516 6274707 0.0464770678179711 0.32452844928987673 chr12 133851895 6314749 0.04717713559453155 0.27755091375590024 chr13 115169878 4103089 0.03562640745351836 0.2329274698501171 chr14 107349540 4070921 0.03792210940074825 0.2468562927981498 chr15 102531392 3910969 0.0381441129756631 0.23761480416744615 chr16 90354753 3926835 0.043460192957419735 0.28035834191527187 chr17 81195210 3630512 0.04471337656494761 0.2801580923723936 chr18 78077248 3593198 0.04602106365224348 0.5729291877283819 chr19 59128983 2689490 0.04548513881931641 0.55886121904603 chr20 63025520 2936162 0.04658687465014172 0.2780329167024615 chr21 48129895 1971151 0.04095481612831277 0.3079399680630811 chr22 51304566 1559512 0.03039713853149055 0.21372498053750383 chrMT 16571 13268 0.800675879548609 1.0371715230324454 chrX 155270560 7421097 0.04779461734407347 0.2974142955660573 chrY 59373566 499954 0.008420481262654832 0.34919424844147606