BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174027.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,910,938 number of mapped reads = 1,873,829 (98.06%) number of supplementary alignments = 200,342 (10.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 934,871 number of mapped paired reads (second in pair) = 938,958 number of mapped paired reads (both in pair) = 1,849,840 number of mapped paired reads (singletons) = 23,989 number of mapped bases = 223,481,760 bp number of sequenced bases = 223,371,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,457,508 duplication rate = 64.39% >>>>>>> Insert size mean insert size = 939,112.1527 std insert size = 9,084,791.034 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.6043 >>>>>>> ACTG content number of A's = 67,892,780 bp (30.39%) number of C's = 43,167,322 bp (19.33%) number of T's = 67,802,476 bp (30.35%) number of G's = 44,506,510 bp (19.92%) number of N's = 2,818 bp (0%) GC percentage = 39.25% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 2,121,950 number of insertions = 23,914 mapped reads with insertion percentage = 1.24% number of deletions = 41,370 mapped reads with deletion percentage = 2.14% homopolymer indels = 44.24% >>>>>>> Coverage mean coverageData = 0.0722X std coverageData = 1.2482X There is a 1.58% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 22107019 0.0886939374967495 1.1211232187424498 chr2 243199373 22441762 0.09227721981010206 3.177605278511273 chr3 198022430 15783354 0.07970487989668645 0.8192037340628674 chr4 191154276 10298659 0.053876163356136486 0.7458616328356684 chr5 180915260 15272735 0.08441927452664855 0.8447332472302219 chr6 171115067 13690029 0.08000481336924001 0.8337239917234639 chr7 159138663 14028094 0.08815013105897465 1.339876734360529 chr8 146364022 10081581 0.06888018559643025 0.852004825462282 chr9 141213431 8538595 0.06046588443842852 0.7738957743744618 chr10 135534747 9802911 0.07232765926806946 1.3145122254039474 chr11 135006516 10417632 0.07716391999923915 0.8076370877275465 chr12 133851895 7795129 0.05823697154231548 0.6915246481446174 chr13 115169878 7736640 0.06717589819796457 0.7659965657139413 chr14 107349540 5446992 0.05074071113858522 0.6486890028195685 chr15 102531392 7206050 0.07028140220704308 0.7518666895827585 chr16 90354753 9647001 0.10676805236798113 1.14400202239565 chr17 81195210 4781300 0.05888647864818627 0.7283836817170853 chr18 78077248 3863556 0.049483762542450266 0.9928834899579976 chr19 59128983 3888059 0.06575555341447357 1.1339611391878486 chr20 63025520 6777183 0.10753077483533655 0.9382251346949467 chr21 48129895 3445111 0.07157944142616558 0.779560117756869 chr22 51304566 1759247 0.034290261806327334 0.4991417830000164 chrMT 16571 688036 41.52048759881721 38.41680550645086 chrX 155270560 7702246 0.049605321189026434 0.6446439274834752 chrY 59373566 282839 0.004763719261868152 0.24021945409567952