BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231745.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 829,823 number of mapped reads = 615,748 (74.2%) number of supplementary alignments = 5,408 (0.65%) number of secondary alignments = 0 number of mapped bases = 40,172,309 bp number of sequenced bases = 40,149,100 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,489 duplication rate = 6.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0314 >>>>>>> ACTG content number of A's = 11,383,667 bp (28.35%) number of C's = 6,777,798 bp (16.88%) number of T's = 13,475,765 bp (33.56%) number of G's = 8,509,778 bp (21.2%) number of N's = 2,092 bp (0.01%) GC percentage = 38.08% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 355,508 number of insertions = 3,925 mapped reads with insertion percentage = 0.63% number of deletions = 12,880 mapped reads with deletion percentage = 2.06% homopolymer indels = 44.33% >>>>>>> Coverage mean coverageData = 0.013X std coverageData = 0.3373X There is a 0.98% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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 2893166 0.011607457539694555 0.2332455521579981 chr2 243199373 3525867 0.014497845765416508 0.18921997279263278 chr3 198022430 2238606 0.011304810268210525 0.13331089920030334 chr4 191154276 878163 0.004594001339525358 0.10496371623891211 chr5 180915260 2657574 0.014689606614721169 0.15641288533538458 chr6 171115067 3073643 0.01796243343083283 0.19391252954338406 chr7 159138663 1859832 0.01168686455534693 0.20956465481198505 chr8 146364022 3023105 0.020654700237740117 1.3459712056475506 chr9 141213431 2440582 0.017282931111559777 0.1926798037052637 chr10 135534747 1573816 0.011611900526143307 0.16246550503878662 chr11 135006516 864320 0.006402061364208524 0.1067085884437971 chr12 133851895 1622305 0.012120149662431003 0.1386558141380628 chr13 115169878 1242814 0.010791137592418044 0.13305458217244429 chr14 107349540 2007103 0.01869689427639839 0.17553275591024498 chr15 102531392 613893 0.005987366288755741 0.09581096197490761 chr16 90354753 879106 0.009729493699130582 0.12977219063064538 chr17 81195210 1235388 0.015215035468225281 0.15833784160918615 chr18 78077248 702408 0.008996321181812145 0.27907502691808056 chr19 59128983 966395 0.01634384613041628 0.18835146224827004 chr20 63025520 1875277 0.029754248755107456 0.2190112031563289 chr21 48129895 1514741 0.031471936516794814 0.23097510112265238 chr22 51304566 400471 0.00780575748365165 0.10728723227174142 chrMT 16571 79784 4.814676241626938 4.174837899318891 chrX 155270560 1846466 0.011891925938825751 0.1407105917085864 chrY 59373566 157484 0.0026524261655430973 0.08449155363275705