BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004054.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 = 2,504,187 number of mapped reads = 2,212,224 (88.34%) number of supplementary alignments = 13,577 (0.54%) number of secondary alignments = 0 number of mapped bases = 148,035,466 bp number of sequenced bases = 147,977,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,768 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8741 >>>>>>> ACTG content number of A's = 40,702,397 bp (27.51%) number of C's = 28,293,482 bp (19.12%) number of T's = 45,657,801 bp (30.85%) number of G's = 33,299,359 bp (22.5%) number of N's = 24,842 bp (0.02%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,261,278 number of insertions = 10,231 mapped reads with insertion percentage = 0.46% number of deletions = 33,015 mapped reads with deletion percentage = 1.48% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 0.0478X std coverageData = 0.379X There is a 4.02% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% 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 11538234 0.04629169609972607 0.6401631535944994 chr2 243199373 11570437 0.0475759326895962 0.41322078414009167 chr3 198022430 10443785 0.052740414305591544 0.26234614689195057 chr4 191154276 9612491 0.05028656016044339 0.2762287266147509 chr5 180915260 7633726 0.04219503650493607 0.23655910204063857 chr6 171115067 9032564 0.05278649132633072 0.2939777286558319 chr7 159138663 9606079 0.06036294900881504 0.6111157028646161 chr8 146364022 10482355 0.07161838583528403 0.4278479123117624 chr9 141213431 6403889 0.045349007914126806 0.3786250314311861 chr10 135534747 5510160 0.04065496208142108 0.317846892589027 chr11 135006516 6823778 0.05054406411020932 0.3519825862578786 chr12 133851895 6829498 0.05102279650205924 0.26560058208233206 chr13 115169878 4836700 0.04199622404740239 0.2374823594086111 chr14 107349540 3892450 0.03625958713935803 0.24634558790084557 chr15 102531392 4427338 0.043180316912112146 0.24741157895581165 chr16 90354753 4203463 0.046521769585270184 0.27490935899688757 chr17 81195210 3618921 0.044570621838406474 0.27397740152388445 chr18 78077248 3957389 0.050685559511523766 0.6465889648593459 chr19 59128983 2383641 0.04031256549770186 0.4478694136241388 chr20 63025520 3735683 0.05927254547046974 0.29641424741514993 chr21 48129895 1886881 0.03920392928345262 0.2491140767692791 chr22 51304566 1062783 0.02071517377225255 0.1616292000217922 chrMT 16571 12083 0.7291654094502444 0.961406603551364 chrX 155270560 8197171 0.05279282176865981 0.29869791015869196 chrY 59373566 333967 0.005624843217266081 0.11963178223880999