BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524306.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 = 1,098,922 number of mapped reads = 1,009,006 (91.82%) number of supplementary alignments = 4,129 (0.38%) number of secondary alignments = 0 number of mapped bases = 58,951,977 bp number of sequenced bases = 58,936,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,984 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2502 >>>>>>> ACTG content number of A's = 14,335,017 bp (24.32%) number of C's = 11,795,479 bp (20.01%) number of T's = 18,146,893 bp (30.79%) number of G's = 14,651,412 bp (24.86%) number of N's = 8,046 bp (0.01%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 293,627 number of insertions = 3,688 mapped reads with insertion percentage = 0.36% number of deletions = 9,397 mapped reads with deletion percentage = 0.93% homopolymer indels = 43.03% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.1983X There is a 1.76% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5028761 0.020175520445343244 0.34658760516733006 chr2 243199373 3729177 0.015333826539100493 0.23860588648460457 chr3 198022430 4077187 0.020589521096170772 0.1509571122881868 chr4 191154276 3011990 0.015756853903702368 0.14345295394878455 chr5 180915260 3438081 0.019003819799391163 0.14571760533223355 chr6 171115067 3679293 0.02150186459033441 0.16307257650080934 chr7 159138663 2701921 0.016978407063781856 0.21115511081100038 chr8 146364022 6100222 0.041678425590135806 0.2581089420581136 chr9 141213431 2455112 0.017385825006971185 0.1572222374878259 chr10 135534747 3025452 0.02232233480319257 0.19611974509183544 chr11 135006516 2856812 0.02116054902120428 0.1703110741451765 chr12 133851895 2344544 0.01751595672216669 0.1403321071955496 chr13 115169878 1481478 0.012863415553848203 0.11881060289336218 chr14 107349540 1229784 0.011455885139330825 0.11818496234651203 chr15 102531392 1813715 0.01768936288312559 0.14169979914776912 chr16 90354753 1912869 0.02117065164242107 0.15776354937621503 chr17 81195210 1739383 0.021422236607307254 0.16343196415199798 chr18 78077248 1358950 0.017405198502898053 0.24593005710986307 chr19 59128983 1086059 0.01836762523042211 0.23917442095052807 chr20 63025520 1390076 0.02205576407778944 0.15766135526523942 chr21 48129895 855173 0.017768021309832484 0.14950930884101443 chr22 51304566 455603 0.008880359693521236 0.09875241218023716 chrMT 16571 222124 13.404381147788305 7.7655517968238765 chrX 155270560 2785885 0.017942132752016865 0.15023131028754755 chrY 59373566 172326 0.0029024027291875984 0.09515481154650994