BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524759.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 = 1,644,288 number of mapped reads = 1,478,156 (89.9%) number of supplementary alignments = 4,933 (0.3%) number of secondary alignments = 0 number of mapped bases = 84,176,913 bp number of sequenced bases = 84,151,149 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,431 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2909 >>>>>>> ACTG content number of A's = 21,303,564 bp (25.32%) number of C's = 17,011,043 bp (20.21%) number of T's = 25,763,733 bp (30.62%) number of G's = 20,062,506 bp (23.84%) number of N's = 10,303 bp (0.01%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 423,623 number of insertions = 6,408 mapped reads with insertion percentage = 0.43% number of deletions = 16,138 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.59% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2314X There is a 2.43% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 6749668 0.02707984426646624 0.2677260937581913 chr2 243199373 7114467 0.029253640386646886 0.3699764626681463 chr3 198022430 5440638 0.027474857267431776 0.18351169054941877 chr4 191154276 5317273 0.027816657368417957 0.20780672533155345 chr5 180915260 4966490 0.027452023671192802 0.18217992947418749 chr6 171115067 4777987 0.02792265511020137 0.20183867412128875 chr7 159138663 4595009 0.028874246605930076 0.2746134296862328 chr8 146364022 4172949 0.028510756557373094 0.21188858710560587 chr9 141213431 3570683 0.02528571804193328 0.20346516620597369 chr10 135534747 4097598 0.030232822878992056 0.2759948085622777 chr11 135006516 3819471 0.028291012264919126 0.21884949537121823 chr12 133851895 3828598 0.02860324091788166 0.1891628757673875 chr13 115169878 2595459 0.022535918636642126 0.16602550271823316 chr14 107349540 2534863 0.02361317058275238 0.17269830883442774 chr15 102531392 2457425 0.023967537668853654 0.17352895195519744 chr16 90354753 2596186 0.028733253246788246 0.20530862870973152 chr17 81195210 2461576 0.03031676375983263 0.20020048317490047 chr18 78077248 2154756 0.0275977452483981 0.3014506069836803 chr19 59128983 1929476 0.032631645296520656 0.25875765248674587 chr20 63025520 1855874 0.029446389335621506 0.19920098115593624 chr21 48129895 1100641 0.022868136321510777 0.18498858108936264 chr22 51304566 1105517 0.021548121077566467 0.16402801852165796 chrMT 16571 17672 1.066441373483797 1.3202210351266221 chrX 155270560 4631615 0.029829318577842445 0.2045564577820251 chrY 59373566 285022 0.00480048646564365 0.13222833760325373