BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240235.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 = 3,176,162 number of mapped reads = 2,535,687 (79.83%) number of supplementary alignments = 19,506 (0.61%) number of secondary alignments = 0 number of mapped bases = 166,973,372 bp number of sequenced bases = 166,893,097 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 490,572 duplication rate = 13.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.871 >>>>>>> ACTG content number of A's = 46,750,931 bp (28.01%) number of C's = 30,494,393 bp (18.27%) number of T's = 53,619,029 bp (32.13%) number of G's = 35,966,257 bp (21.55%) number of N's = 62,487 bp (0.04%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,454,293 number of insertions = 12,238 mapped reads with insertion percentage = 0.48% number of deletions = 46,023 mapped reads with deletion percentage = 1.79% homopolymer indels = 48.4% >>>>>>> Coverage mean coverageData = 0.0539X std coverageData = 0.6271X There is a 1.89% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 13711153 0.055009503867996384 0.8926249076502386 chr2 243199373 18010749 0.07405754701513971 0.7223201009109705 chr3 198022430 10412995 0.05258492686914305 0.5130247932681026 chr4 191154276 10886382 0.05695076368576762 0.5387355323974736 chr5 180915260 8580065 0.047425877728611725 0.48415713120841775 chr6 171115067 8844454 0.051687172585450934 0.5406223912923287 chr7 159138663 9705324 0.06098658752713035 0.8363355683959417 chr8 146364022 9521937 0.06505654101251741 0.8308826147043585 chr9 141213431 5983151 0.04236956044216502 0.5347829862862054 chr10 135534747 7976133 0.058849359124121876 0.6578013278823058 chr11 135006516 7475418 0.05537079410300463 0.6393862812463608 chr12 133851895 7996491 0.05974133575023349 0.5452488756704749 chr13 115169878 4320209 0.037511622613683765 0.43992426973603077 chr14 107349540 5260729 0.04900560356383456 0.5013438380450517 chr15 102531392 4799015 0.04680532377830197 0.49453246469234297 chr16 90354753 5081374 0.056238037638152806 0.5275228369994209 chr17 81195210 3929516 0.04839590906902021 0.49404907390815883 chr18 78077248 4104015 0.052563520169153506 0.8203491016607979 chr19 59128983 2967384 0.05018493215078636 0.6342420046445557 chr20 63025520 3441120 0.05459883551932614 0.5239714109843451 chr21 48129895 2765203 0.057452919853658524 0.5416549380179433 chr22 51304566 1528085 0.029784580966926023 0.3615526642427246 chrMT 16571 34039 2.05413071027699 3.290676992610963 chrX 155270560 9180578 0.0591263276180623 0.5622985222030027 chrY 59373566 457853 0.00771139466340964 0.18458241142586934