BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716342.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 = 1,847,495 number of mapped reads = 1,689,405 (91.44%) number of supplementary alignments = 10,980 (0.59%) number of secondary alignments = 0 number of mapped bases = 99,252,747 bp number of sequenced bases = 99,224,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,676 duplication rate = 3.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1774 >>>>>>> ACTG content number of A's = 24,971,143 bp (25.17%) number of C's = 19,419,990 bp (19.57%) number of T's = 30,862,399 bp (31.1%) number of G's = 23,970,003 bp (24.16%) number of N's = 1,287 bp (0%) GC percentage = 43.73% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 485,960 number of insertions = 6,933 mapped reads with insertion percentage = 0.41% number of deletions = 17,557 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.49% >>>>>>> Coverage mean coverageData = 0.0321X std coverageData = 0.2751X There is a 2.78% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% 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 8001851 0.032103635160050416 0.41478785212386565 chr2 243199373 8860078 0.03643133570085314 0.35004217730562626 chr3 198022430 6576796 0.03321237902191181 0.20429641616496724 chr4 191154276 6212305 0.032498906799238954 0.23429113639565327 chr5 180915260 5701772 0.03151625794308341 0.19952916636147644 chr6 171115067 4890470 0.028580008094786884 0.2065096598595702 chr7 159138663 5803800 0.036470081440862674 0.4054833608936996 chr8 146364022 5284431 0.0361047129464644 0.2912104409040082 chr9 141213431 3988148 0.028241987831879815 0.22765080745476024 chr10 135534747 4843185 0.03573389929299827 0.29224945501474875 chr11 135006516 4521204 0.03348878360804452 0.25436537675870935 chr12 133851895 4581290 0.03422656063255586 0.2108458798661716 chr13 115169878 3024223 0.02625880180232543 0.18191070498018924 chr14 107349540 3027572 0.02820293407871147 0.1942771218518906 chr15 102531392 2970700 0.02897356548129182 0.19477853258417396 chr16 90354753 3107340 0.03439044319007767 0.22355546268942103 chr17 81195210 2720357 0.033503909898133157 0.22596114133689096 chr18 78077248 2579307 0.03303532163428711 0.40038270276848414 chr19 59128983 1988435 0.03362877051343839 0.34473683163974905 chr20 63025520 2174090 0.034495391707993844 0.21400558015211069 chr21 48129895 1330740 0.02764892796878115 0.21002826254790063 chr22 51304566 1253487 0.024432269829550844 0.1761934384854955 chrMT 16571 35182 2.1231066320680707 1.9663660778951482 chrX 155270560 5468252 0.0352175711867079 0.22596856462125725 chrY 59373566 307732 0.005182979913990681 0.1600557648094791