BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354851.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 20,277,036 number of mapped reads = 20,065,478 (98.96%) number of supplementary alignments = 368,452 (1.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,052,033 number of mapped paired reads (second in pair) = 10,013,445 number of mapped paired reads (both in pair) = 19,986,950 number of mapped paired reads (singletons) = 78,528 number of mapped bases = 2,782,472,646 bp number of sequenced bases = 2,780,791,503 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,536,272 duplication rate = 27.65% >>>>>>> Insert size mean insert size = 141,854.886 std insert size = 4,196,739.8571 median insert size = 270 >>>>>>> Mapping quality mean mapping quality = 53.9288 >>>>>>> ACTG content number of A's = 799,154,133 bp (28.74%) number of C's = 583,696,931 bp (20.99%) number of T's = 803,471,448 bp (28.89%) number of G's = 594,421,740 bp (21.38%) number of N's = 47,251 bp (0%) GC percentage = 42.37% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 23,140,151 number of insertions = 545,974 mapped reads with insertion percentage = 2.47% number of deletions = 518,768 mapped reads with deletion percentage = 2.4% homopolymer indels = 39% >>>>>>> Coverage mean coverageData = 0.8988X std coverageData = 18.1453X There is a 39.77% of reference with a coverageData >= 1X There is a 21.89% of reference with a coverageData >= 2X There is a 10.01% of reference with a coverageData >= 3X There is a 5.47% of reference with a coverageData >= 4X There is a 2.55% of reference with a coverageData >= 5X There is a 1.41% of reference with a coverageData >= 6X There is a 0.7% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% 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 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 225184141 0.9034446538048946 24.205675871678864 chr2 243199373 242785753 0.9982992554836891 36.371618151287684 chr3 198022430 178226270 0.9000307187423162 1.74728091790194 chr4 191154276 196386585 1.0273721786898453 25.866298197686167 chr5 180915260 162231221 0.8967249141946345 1.5779930234176474 chr6 171115067 153604326 0.8976668664717876 3.2365200925834356 chr7 159138663 146438547 0.9201946543939482 11.010235355663102 chr8 146364022 139616785 0.9539009866782698 25.62010611153567 chr9 141213431 117221226 0.8300996949787305 12.085358239981092 chr10 135534747 157445885 1.1616643590296443 31.6669108521287 chr11 135006516 126194458 0.9347286467269476 3.690865035605444 chr12 133851895 119949174 0.8961335511910384 1.5695739046025214 chr13 115169878 84432113 0.7331093378426605 1.3334726758084459 chr14 107349540 82100876 0.7647995138125417 2.3298449666289813 chr15 102531392 77515614 0.7560183519209415 1.354208609178387 chr16 90354753 85907856 0.9507840279304399 6.501292930432168 chr17 81195210 75077714 0.9246569348117949 5.050212624797403 chr18 78077248 77193623 0.9886826825658609 15.30532385157562 chr19 59128983 53714483 0.9084290017299976 13.80056236451759 chr20 63025520 58545647 0.9289196979255387 8.533473260912602 chr21 48129895 40095534 0.8330692182062729 13.246458224752454 chr22 51304566 34702915 0.6764098735383514 2.5263313736278663 chrMT 16571 27532420 1661.4821072958784 514.6298588244917 chrX 155270560 73745845 0.4749505959146409 1.5122757381663126 chrY 59373566 46623635 0.7852591336690136 27.963006136987527