BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716815.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 = 949,105 number of mapped reads = 767,128 (80.83%) number of supplementary alignments = 2,832 (0.3%) number of secondary alignments = 0 number of mapped bases = 41,960,841 bp number of sequenced bases = 41,948,758 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,152 duplication rate = 1.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.8397 >>>>>>> ACTG content number of A's = 9,869,653 bp (23.53%) number of C's = 8,274,935 bp (19.73%) number of T's = 12,463,359 bp (29.71%) number of G's = 11,339,909 bp (27.03%) number of N's = 902 bp (0%) GC percentage = 46.76% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 220,681 number of insertions = 2,763 mapped reads with insertion percentage = 0.36% number of deletions = 7,103 mapped reads with deletion percentage = 0.92% homopolymer indels = 36.07% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 0.1375X There is a 1.26% of reference with a coverageData >= 1X There is a 0.07% 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 3409119 0.013677474448498967 0.14132581490193816 chr2 243199373 3438131 0.014137088256391187 0.17326638066438413 chr3 198022430 2648507 0.013374782846569452 0.12777282968447978 chr4 191154276 2580553 0.013499844492100193 0.13729389182075255 chr5 180915260 2438937 0.013481101594193879 0.1244504770204487 chr6 171115067 2334074 0.013640376858222543 0.12726302533645645 chr7 159138663 2348248 0.014755986733406199 0.14925694057023495 chr8 146364022 1960075 0.013391781485753377 0.1289000512941577 chr9 141213431 1737980 0.012307469535245552 0.12562809141564063 chr10 135534747 2083247 0.015370575045231758 0.16494973859583226 chr11 135006516 1855220 0.013741707103974151 0.13837818970801183 chr12 133851895 1895593 0.014161868982131332 0.12779837850011475 chr13 115169878 1219300 0.01058696962412342 0.11127933868157408 chr14 107349540 1255757 0.011697833078744446 0.11888637594175963 chr15 102531392 1228500 0.011981696298437068 0.11849561716738802 chr16 90354753 1411509 0.015621856660932933 0.14055482477120707 chr17 81195210 1415522 0.017433565354409455 0.14539429990930122 chr18 78077248 1080431 0.013837974924526028 0.15639252004154872 chr19 59128983 1130997 0.019127624772440278 0.16224157899518823 chr20 63025520 976480 0.015493406480422533 0.13571722292901572 chr21 48129895 549989 0.011427180549635523 0.12375710095757637 chr22 51304566 640527 0.012484795212964086 0.12205293577015525 chrMT 16571 5305 0.32013758976525253 0.6501421633979566 chrX 155270560 2167911 0.013962150970538137 0.1340379759783198 chrY 59373566 148929 0.0025083384750715495 0.08116492934329517