BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237579.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 = 1,143,042 number of mapped reads = 953,451 (83.41%) number of supplementary alignments = 5,361 (0.47%) number of secondary alignments = 0 number of mapped bases = 59,960,726 bp number of sequenced bases = 59,925,804 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,813 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0883 >>>>>>> ACTG content number of A's = 15,367,490 bp (25.64%) number of C's = 10,884,293 bp (18.16%) number of T's = 18,419,355 bp (30.74%) number of G's = 15,216,908 bp (25.39%) number of N's = 37,758 bp (0.06%) GC percentage = 43.56% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 568,880 number of insertions = 5,591 mapped reads with insertion percentage = 0.58% number of deletions = 21,107 mapped reads with deletion percentage = 2.18% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.0194X std coverageData = 0.2157X There is a 1.64% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.05% 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 5200041 0.020862700277886167 0.2816059424839375 chr2 243199373 5270784 0.02167268745384471 0.28585496144215344 chr3 198022430 4213756 0.02127918539329105 0.17745294509034337 chr4 191154276 3847275 0.020126544278821153 0.17896946639959382 chr5 180915260 3258153 0.0180092768293841 0.15877295022452223 chr6 171115067 3099106 0.018111239730864846 0.17362923929888235 chr7 159138663 3533360 0.022203026803109437 0.3005405841163343 chr8 146364022 3121708 0.02132838355589873 0.21122102350425923 chr9 141213431 2478690 0.017552792127825293 0.23207825414757516 chr10 135534747 2620827 0.019336938003064262 0.21207151945904787 chr11 135006516 2525643 0.018707563714924692 0.23193679249022123 chr12 133851895 3470815 0.025930264192374715 0.20055285016624316 chr13 115169878 1984015 0.017226856834909557 0.15993860091609402 chr14 107349540 1675271 0.015605758534223808 0.17370374772170966 chr15 102531392 1834478 0.017891866717268404 0.16920935189321604 chr16 90354753 1636458 0.018111476659119417 0.18065152176007399 chr17 81195210 1480992 0.018239893708015535 0.17028909639168202 chr18 78077248 1526292 0.01954848613516706 0.3138946808932446 chr19 59128983 1219490 0.020624234311623454 0.21925412771625113 chr20 63025520 1225282 0.01944104546856575 0.17434669771525207 chr21 48129895 724154 0.015045825468765307 0.16212090626107378 chr22 51304566 627606 0.012232946283962327 0.13332892435372054 chrMT 16571 55830 3.369138857039406 3.0140379712545875 chrX 155270560 3117833 0.02008000099954557 0.18208652417778828 chrY 59373566 212867 0.0035852150096559805 0.09411080180083525