BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236129.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,764,742 number of mapped reads = 1,497,640 (84.86%) number of supplementary alignments = 8,057 (0.46%) number of secondary alignments = 0 number of mapped bases = 99,160,991 bp number of sequenced bases = 99,102,439 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,430 duplication rate = 2.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6604 >>>>>>> ACTG content number of A's = 27,626,444 bp (27.88%) number of C's = 17,463,962 bp (17.62%) number of T's = 31,964,067 bp (32.25%) number of G's = 21,988,234 bp (22.19%) number of N's = 59,732 bp (0.06%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 883,595 number of insertions = 7,733 mapped reads with insertion percentage = 0.51% number of deletions = 33,564 mapped reads with deletion percentage = 2.21% homopolymer indels = 45.9% >>>>>>> Coverage mean coverageData = 0.032X std coverageData = 0.4265X There is a 2.81% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 6360682 0.025519222277083115 0.6822443781919554 chr2 243199373 7280025 0.029934390496968923 0.3772948093799635 chr3 198022430 8354019 0.0421872360620966 0.22517121326953202 chr4 191154276 6149496 0.03217032926849096 0.21775136265373082 chr5 180915260 4612193 0.025493664824072882 0.18317999700612864 chr6 171115067 8182826 0.04782060483312086 0.3514342970321069 chr7 159138663 6626637 0.0416406476910014 0.44594173374896656 chr8 146364022 5885947 0.04021443876419302 1.2043218304811873 chr9 141213431 4876349 0.034531764899898225 0.3461089966478213 chr10 135534747 3301714 0.024360646056320892 0.2827026686583377 chr11 135006516 3780460 0.028002055841512125 0.2500611170859505 chr12 133851895 3129383 0.023379444870765556 0.17816376724614658 chr13 115169878 4758226 0.041314847967452044 0.22296352598302996 chr14 107349540 2737832 0.025503900622210397 0.200259037553606 chr15 102531392 2599986 0.025357950860552054 0.18116389691773266 chr16 90354753 3105969 0.03437526966622331 0.23915220216298258 chr17 81195210 2662501 0.032791355549175866 0.23475633183650849 chr18 78077248 3638278 0.04659844055979022 0.6306907542600734 chr19 59128983 2246745 0.0379973557130181 0.4747759449026075 chr20 63025520 1526813 0.024225313809390227 0.18003116182776008 chr21 48129895 1972720 0.04098741540990272 0.24325538643397432 chr22 51304566 763359 0.014878968082489967 0.1314829904565314 chrMT 16571 86146 5.198599963792167 4.167794174440664 chrX 155270560 4278239 0.027553446062151127 0.208423989378642 chrY 59373566 244446 0.004117084697253993 0.11266023647268802