BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004156.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 = 2,195,746 number of mapped reads = 1,961,354 (89.33%) number of supplementary alignments = 20,220 (0.92%) number of secondary alignments = 0 number of mapped bases = 130,639,692 bp number of sequenced bases = 130,571,187 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,368 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5446 >>>>>>> ACTG content number of A's = 37,448,843 bp (28.68%) number of C's = 23,787,687 bp (18.22%) number of T's = 41,653,800 bp (31.9%) number of G's = 27,671,643 bp (21.19%) number of N's = 9,214 bp (0.01%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,193,907 number of insertions = 10,501 mapped reads with insertion percentage = 0.53% number of deletions = 40,709 mapped reads with deletion percentage = 2.05% homopolymer indels = 44.94% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.3877X There is a 3.61% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.01% 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 9869110 0.03959512702678482 0.7069091392066171 chr2 243199373 11143231 0.04581932454241977 0.37840784103479824 chr3 198022430 11930139 0.06024640238987068 0.2752377334650964 chr4 191154276 10155132 0.05312531957171599 0.28466699832379355 chr5 180915260 7993875 0.04418574198771292 0.240469016915281 chr6 171115067 9464930 0.05531324719640264 0.3046244757048476 chr7 159138663 6493034 0.04080110940733491 0.3139247131274741 chr8 146364022 10350752 0.070719237272668 0.7533337117604562 chr9 141213431 5305912 0.03757370642740066 0.3698233525709152 chr10 135534747 6798310 0.05015916693303747 0.39937044341730904 chr11 135006516 4064234 0.030103984018075097 0.24624736672187006 chr12 133851895 5048775 0.03771911484704792 0.23303089689315437 chr13 115169878 5075547 0.04407009096597289 0.2376067203052999 chr14 107349540 3824004 0.03562198776073004 0.23270815185536955 chr15 102531392 3242253 0.03162205190777084 0.19933285827603273 chr16 90354753 3550933 0.03929990268469884 0.25790487253372235 chr17 81195210 1382255 0.017023849066958505 0.15495601256677732 chr18 78077248 3174065 0.04065288008101925 0.681466622911194 chr19 59128983 1440627 0.024364143046397398 0.5145468306490908 chr20 63025520 2489715 0.03950328374918605 0.23813764577527963 chr21 48129895 1388714 0.028853459996120913 0.22309841467656438 chr22 51304566 764717 0.014905437461453236 0.1339728654476888 chrMT 16571 53572 3.232876712328767 2.8286338978271806 chrX 155270560 5322294 0.03427754752736127 0.2378000999643853 chrY 59373566 313562 0.0052811717591629915 0.15082842644194744