BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717076.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 = 723,411 number of mapped reads = 663,009 (91.65%) number of supplementary alignments = 1,292 (0.18%) number of secondary alignments = 0 number of mapped bases = 38,541,190 bp number of sequenced bases = 38,528,792 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,569 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0848 >>>>>>> ACTG content number of A's = 9,850,423 bp (25.57%) number of C's = 6,799,526 bp (17.65%) number of T's = 12,195,373 bp (31.65%) number of G's = 9,683,088 bp (25.13%) number of N's = 382 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 183,061 number of insertions = 3,097 mapped reads with insertion percentage = 0.47% number of deletions = 7,821 mapped reads with deletion percentage = 1.17% homopolymer indels = 40.99% >>>>>>> Coverage mean coverageData = 0.0124X std coverageData = 0.1396X There is a 1.17% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% 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 4538118 0.018207047917445308 0.1865144307955605 chr2 243199373 3941577 0.01620718405388323 0.17668432709878798 chr3 198022430 2495365 0.012601426010174705 0.11866480384435159 chr4 191154276 1659120 0.008679481488554302 0.09974940459933578 chr5 180915260 2783850 0.015387590853308892 0.12942940501883116 chr6 171115067 1428228 0.008346594049488348 0.09983765335296689 chr7 159138663 2587548 0.01625970679419369 0.22495118142909493 chr8 146364022 1717705 0.011735841749415714 0.12299853752828199 chr9 141213431 1010931 0.0071588870324948055 0.10449094277036979 chr10 135534747 1804404 0.01331322070494587 0.1630871791960512 chr11 135006516 1645346 0.012187159914562939 0.13408957642506056 chr12 133851895 1516206 0.011327489984359205 0.11163570867442832 chr13 115169878 1160358 0.010075186499720005 0.10492349564764297 chr14 107349540 806545 0.007513259954350992 0.09245232844276238 chr15 102531392 1594031 0.015546760547247813 0.13049677040020022 chr16 90354753 1179693 0.01305623623363787 0.1262763744998331 chr17 81195210 1391407 0.01713656507569843 0.1416137727971083 chr18 78077248 1250612 0.016017623981828866 0.19229968969893602 chr19 59128983 601032 0.010164761332018851 0.14154974904917353 chr20 63025520 1028096 0.01631237631994151 0.1335222021889246 chr21 48129895 486491 0.01010787578073877 0.10776326800627627 chr22 51304566 401636 0.007828465014205558 0.0923193591119686 chrMT 16571 664 0.04007000181039165 0.19612342227614443 chrX 155270560 1428126 0.009197661166418155 0.10793583381584268 chrY 59373566 84101 0.0014164721047747074 0.045768490434111145