BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013183.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 = 2,104,151 number of mapped reads = 1,521,229 (72.3%) number of supplementary alignments = 8,817 (0.42%) number of secondary alignments = 0 number of mapped bases = 89,614,620 bp number of sequenced bases = 89,573,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,815 duplication rate = 8.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6515 >>>>>>> ACTG content number of A's = 26,016,484 bp (29.04%) number of C's = 16,833,830 bp (18.79%) number of T's = 27,433,266 bp (30.63%) number of G's = 19,289,504 bp (21.53%) number of N's = 727 bp (0%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 743,674 number of insertions = 6,284 mapped reads with insertion percentage = 0.41% number of deletions = 24,636 mapped reads with deletion percentage = 1.6% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2947X There is a 2.01% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 6652661 0.026690649649374395 0.34935528607919625 chr2 243199373 8351603 0.034340561396101955 0.3651165512804619 chr3 198022430 7240799 0.03656554967030755 0.2613612061250188 chr4 191154276 6105069 0.03193791490178331 0.25241560074711805 chr5 180915260 4903314 0.027102821508810257 0.226798424115324 chr6 171115067 5717381 0.03341249312662806 0.28406165117691834 chr7 159138663 5382934 0.033825431849958426 0.464754617926008 chr8 146364022 5302226 0.03622629337146802 0.44042689020082565 chr9 141213431 3693846 0.02615789428698181 0.2618845584069408 chr10 135534747 3509910 0.025896753988849813 0.27438619521039037 chr11 135006516 3759771 0.027848811386259314 0.256928386076055 chr12 133851895 4214456 0.03148596439370545 0.2441258739584263 chr13 115169878 2283390 0.019826277839766402 0.19190493942218168 chr14 107349540 3328693 0.031007985688620558 0.24629132425147363 chr15 102531392 2080207 0.02028848881716148 0.20222797543066226 chr16 90354753 2167934 0.023993580061029 0.2126984957842295 chr17 81195210 2499157 0.03077961126031942 0.24627114685575263 chr18 78077248 2363480 0.030271046438522013 0.3804193001900923 chr19 59128983 1402700 0.023722714797918983 0.28714152472457066 chr20 63025520 1600159 0.02538906462017291 0.22198757230887728 chr21 48129895 1259727 0.026173483237393307 0.2243823990494989 chr22 51304566 912140 0.01777892439437067 0.17517351747035342 chrMT 16571 59409 3.585118580652948 3.5066763461035464 chrX 155270560 4633025 0.02983839950084549 0.2488375248809939 chrY 59373566 190629 0.003210671226990139 0.07829872371935258