BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716171.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 = 681,553 number of mapped reads = 635,951 (93.31%) number of supplementary alignments = 12,546 (1.84%) number of secondary alignments = 0 number of mapped bases = 50,254,342 bp number of sequenced bases = 50,231,355 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,589 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6121 >>>>>>> ACTG content number of A's = 12,841,004 bp (25.56%) number of C's = 10,043,405 bp (19.99%) number of T's = 15,222,962 bp (30.31%) number of G's = 12,120,258 bp (24.13%) number of N's = 3,726 bp (0.01%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 326,862 number of insertions = 4,735 mapped reads with insertion percentage = 0.73% number of deletions = 11,899 mapped reads with deletion percentage = 1.84% homopolymer indels = 41.87% >>>>>>> Coverage mean coverageData = 0.0162X std coverageData = 0.1702X There is a 1.51% of reference with a coverageData >= 1X There is a 0.08% 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 4043289 0.016221781048240597 0.26430359345973936 chr2 243199373 4257283 0.017505320624325787 0.1922003454247311 chr3 198022430 3388743 0.017112925035815386 0.13691778604302152 chr4 191154276 3275248 0.017134055635773485 0.1566446461021362 chr5 180915260 3054677 0.01688457347379099 0.13672842923346618 chr6 171115067 2849158 0.016650538435636412 0.14122648668303736 chr7 159138663 2714104 0.0170549629413438 0.20008852885579823 chr8 146364022 2580144 0.01762826659682801 0.20157496060137103 chr9 141213431 2085704 0.01476986987165548 0.15911390008357848 chr10 135534747 2427351 0.017909436906242204 0.18592289630111522 chr11 135006516 2291551 0.01697363259118545 0.16734621386583812 chr12 133851895 2296473 0.017156820977394457 0.13771434111940786 chr13 115169878 1536727 0.013343133002190035 0.12057500435664008 chr14 107349540 1508114 0.014048630296878776 0.12652722473282496 chr15 102531392 1488107 0.014513672066404795 0.12604141860428172 chr16 90354753 1501533 0.016618196056603685 0.1396822157056113 chr17 81195210 1372867 0.016908226482818384 0.14420032048796505 chr18 78077248 1366521 0.017502166572264433 0.21580974520605925 chr19 59128983 1003488 0.016971169620827065 0.19637422573635088 chr20 63025520 1088686 0.017273732925963958 0.14108188574462308 chr21 48129895 661170 0.01373720013309815 0.1329244513341517 chr22 51304566 611681 0.011922545061583797 0.1146803034012487 chrMT 16571 4293 0.2590670448373665 0.6016463698804908 chrX 155270560 2697070 0.017370131208388765 0.14772443398574936 chrY 59373566 150360 0.002532440109795662 0.09717809774158973