BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716472.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 = 1,062,525 number of mapped reads = 958,053 (90.17%) number of supplementary alignments = 5,010 (0.47%) number of secondary alignments = 0 number of mapped bases = 55,184,278 bp number of sequenced bases = 55,168,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,536 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1438 >>>>>>> ACTG content number of A's = 13,662,643 bp (24.77%) number of C's = 10,505,448 bp (19.04%) number of T's = 17,550,528 bp (31.81%) number of G's = 13,449,009 bp (24.38%) number of N's = 637 bp (0%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 276,391 number of insertions = 4,324 mapped reads with insertion percentage = 0.45% number of deletions = 10,186 mapped reads with deletion percentage = 1.06% homopolymer indels = 39.21% >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 0.1952X There is a 1.65% of reference with a coverageData >= 1X There is a 0.09% 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 4301645 0.017258312066552484 0.2459547693251831 chr2 243199373 5045866 0.020747857766886594 0.24023187393765708 chr3 198022430 4124591 0.020828908119145898 0.1590746099833565 chr4 191154276 3137180 0.016411769936028008 0.14439420088107158 chr5 180915260 2822683 0.015602238307592184 0.13164325496171075 chr6 171115067 3149157 0.018403738812783798 0.15111441119117305 chr7 159138663 3259296 0.02048085574276818 0.4039594919515429 chr8 146364022 4440802 0.030340803288392827 0.22004970375133462 chr9 141213431 2332671 0.016518761590036006 0.14970254107807257 chr10 135534747 2702217 0.01993744821761463 0.24692520474736968 chr11 135006516 1896673 0.01404875154322181 0.1419187385534625 chr12 133851895 2627405 0.01962919538793231 0.15756777055206203 chr13 115169878 1032601 0.008965894710768037 0.10014315927783461 chr14 107349540 1823250 0.016984236727982254 0.13933098267106964 chr15 102531392 1341695 0.013085699646016705 0.1223829336690296 chr16 90354753 1708329 0.018906907974171543 0.1504883015103578 chr17 81195210 2338274 0.02879817664120827 0.1838020821639315 chr18 78077248 1162933 0.014894646389176012 0.20373889884250154 chr19 59128983 1127131 0.01906224228480304 0.22870610209010925 chr20 63025520 1249863 0.01983106208405738 0.15445966543399153 chr21 48129895 576205 0.011971873198559855 0.11854677690871078 chr22 51304566 824074 0.01606239101603549 0.1337161491943088 chrMT 16571 55041 3.321525556695432 2.562910348157909 chrX 155270560 1982703 0.012769342752418745 0.13058552371719148 chrY 59373566 121993 0.0020546685708586207 0.06154065780351175