BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004059.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 = 3,388,820 number of mapped reads = 2,956,951 (87.26%) number of supplementary alignments = 29,931 (0.88%) number of secondary alignments = 0 number of mapped bases = 192,601,826 bp number of sequenced bases = 192,503,096 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,246 duplication rate = 4.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0934 >>>>>>> ACTG content number of A's = 52,778,490 bp (27.42%) number of C's = 35,174,955 bp (18.27%) number of T's = 60,886,339 bp (31.63%) number of G's = 43,520,348 bp (22.61%) number of N's = 142,964 bp (0.07%) GC percentage = 40.88% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,702,242 number of insertions = 13,877 mapped reads with insertion percentage = 0.47% number of deletions = 59,276 mapped reads with deletion percentage = 1.98% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.0622X std coverageData = 0.5166X There is a 4.95% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14378942 0.05768869077361296 1.027568671565595 chr2 243199373 14773610 0.060746908257859694 0.5776082580352746 chr3 198022430 17708589 0.08942718761707955 0.3696809491366759 chr4 191154276 13847502 0.07244149746354614 0.3348667432524748 chr5 180915260 8635993 0.04773501693555314 0.26775300088152393 chr6 171115067 14226185 0.08313812015162873 0.4244778087223322 chr7 159138663 12217307 0.07677145685206617 0.5447698669639418 chr8 146364022 11901133 0.08131187458076275 0.7940196013116974 chr9 141213431 5869102 0.04156192480019836 0.403020995269719 chr10 135534747 8961387 0.06611874222925285 0.5385313730597185 chr11 135006516 8744473 0.06477074780597997 0.39147224473304065 chr12 133851895 10671485 0.07972606588797267 0.3456883896506119 chr13 115169878 6734191 0.058471808053838524 0.2888748170723442 chr14 107349540 4139807 0.03856380753937092 0.2697412572708576 chr15 102531392 5749497 0.056075479790618665 0.2886850272160759 chr16 90354753 5458065 0.060407060157643286 0.33450633893246495 chr17 81195210 3871437 0.04768060825262968 0.2846121527180575 chr18 78077248 5129646 0.0656996260933787 0.7870295087750435 chr19 59128983 3032028 0.05127820311064711 0.7064128332415227 chr20 63025520 5231240 0.08300193318516055 0.37817407776163475 chr21 48129895 2401771 0.049901854138680334 0.28410840312337543 chr22 51304566 1388336 0.027060671364026352 0.1932800901042936 chrMT 16571 16319 0.9847927101562971 1.3147475259516683 chrX 155270560 7113263 0.045812052201009645 0.2963830000810885 chrY 59373566 400518 0.00674572923580167 0.13980139066687633