BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234044.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 = 1,836,118 number of mapped reads = 276,277 (15.05%) number of supplementary alignments = 1,717 (0.09%) number of secondary alignments = 0 number of mapped bases = 18,247,392 bp number of sequenced bases = 18,239,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,938 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4549 >>>>>>> ACTG content number of A's = 4,725,962 bp (25.91%) number of C's = 3,403,746 bp (18.66%) number of T's = 6,059,492 bp (33.22%) number of G's = 4,049,477 bp (22.2%) number of N's = 1,167 bp (0.01%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 194,301 number of insertions = 1,479 mapped reads with insertion percentage = 0.53% number of deletions = 4,530 mapped reads with deletion percentage = 1.62% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0059X std coverageData = 0.4124X There is a 0.48% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 1351090 0.005420608360289702 0.14718663308294067 chr2 243199373 1276034 0.005246863856018247 0.4260686383904624 chr3 198022430 2212166 0.01117129004022423 0.2050210566674765 chr4 191154276 784755 0.004105348917227465 0.11337738500989271 chr5 180915260 790874 0.004371516255732104 0.12731140534432864 chr6 171115067 1661800 0.00971159366112395 0.2693520934604615 chr7 159138663 1164627 0.0073183158513779895 0.4479805776367217 chr8 146364022 1023400 0.006992155490233795 0.45868567927891873 chr9 141213431 950982 0.006734359425060637 0.12356857458059226 chr10 135534747 841642 0.006209787664265902 0.11474817446337329 chr11 135006516 694661 0.005145388686276446 0.09701822162066161 chr12 133851895 394119 0.002944440943477117 0.11395786721727745 chr13 115169878 763960 0.006633331677229006 0.6118812669900753 chr14 107349540 792517 0.007382584033429487 0.13502691409050657 chr15 102531392 396540 0.0038674984535467926 0.0941106024829425 chr16 90354753 395254 0.004374468269533092 0.13635105606697231 chr17 81195210 316732 0.0039008705070163623 0.08215192833608762 chr18 78077248 419508 0.005372986506901473 2.0379548056866907 chr19 59128983 399097 0.006749600276399139 0.1855658371593868 chr20 63025520 324153 0.005143202309159845 0.09800564458112355 chr21 48129895 219442 0.00455937001316957 0.09218880906053241 chr22 51304566 120455 0.002347841710618895 0.07986419515783909 chrMT 16571 10364 0.6254299680164143 1.9259071444570406 chrX 155270560 881822 0.005679260769073029 0.10008104099641506 chrY 59373566 61398 0.0010340965540119318 0.24379445352223492