BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716188.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 = 1,348,352 number of mapped reads = 1,201,852 (89.13%) number of supplementary alignments = 4,735 (0.35%) number of secondary alignments = 0 number of mapped bases = 68,787,728 bp number of sequenced bases = 68,766,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,072 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3869 >>>>>>> ACTG content number of A's = 16,297,089 bp (23.7%) number of C's = 13,319,687 bp (19.37%) number of T's = 21,701,105 bp (31.56%) number of G's = 17,447,737 bp (25.37%) number of N's = 532 bp (0%) GC percentage = 44.74% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 366,794 number of insertions = 4,974 mapped reads with insertion percentage = 0.41% number of deletions = 13,403 mapped reads with deletion percentage = 1.11% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.0222X std coverageData = 0.204X There is a 2.04% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5723032 0.022960953826470107 0.245877402240994 chr2 243199373 5356482 0.022025065007054933 0.2772391651306901 chr3 198022430 3972176 0.020059222584027477 0.1551982063510464 chr4 191154276 4258668 0.02227869597852993 0.1705418697354619 chr5 180915260 3906116 0.02159085972073334 0.15577542575484984 chr6 171115067 3677680 0.021492438184885262 0.18530040234486475 chr7 159138663 3926900 0.024675964507757615 0.28436966557370247 chr8 146364022 3556301 0.02429764467664055 0.19883454835119946 chr9 141213431 2261581 0.01601533922081392 0.15251733737884932 chr10 135534747 3032592 0.02237501502105582 0.25805444630423413 chr11 135006516 2440906 0.01807991252807383 0.16889985445699351 chr12 133851895 3422998 0.025573026067356012 0.1708306620584284 chr13 115169878 2050056 0.017800279340401837 0.1416785531334433 chr14 107349540 2311315 0.02153073967527015 0.1634161284771367 chr15 102531392 2523726 0.02461417865076873 0.16854646731703343 chr16 90354753 2387480 0.02642340243019645 0.185283454822772 chr17 81195210 3033298 0.03735809045878445 0.21440590544572843 chr18 78077248 1288314 0.01650050473090445 0.23333467936021052 chr19 59128983 1817842 0.030743671001410594 0.25076353913057536 chr20 63025520 2216050 0.03516115376755321 0.20664018654894692 chr21 48129895 865996 0.017992891943770083 0.15282415633571303 chr22 51304566 623446 0.012151861883014467 0.11714907841283813 chrMT 16571 186527 11.25623076458874 7.621380963748108 chrX 155270560 3744547 0.02411627162290134 0.17253108577396611 chrY 59373566 203699 0.0034308028593061095 0.0995671621782462