BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525181.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 = 2,501,701 number of mapped reads = 2,330,416 (93.15%) number of supplementary alignments = 6,842 (0.27%) number of secondary alignments = 0 number of mapped bases = 136,754,853 bp number of sequenced bases = 136,710,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,756 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0441 >>>>>>> ACTG content number of A's = 36,227,623 bp (26.5%) number of C's = 27,812,562 bp (20.34%) number of T's = 41,494,040 bp (30.35%) number of G's = 31,173,387 bp (22.8%) number of N's = 3,182 bp (0%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 676,039 number of insertions = 10,731 mapped reads with insertion percentage = 0.46% number of deletions = 27,781 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.55% >>>>>>> Coverage mean coverageData = 0.0442X std coverageData = 0.393X There is a 3.85% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 15127455 0.06069174447513212 0.7129892141865083 chr2 243199373 10837496 0.04456218725531007 0.49549659729264617 chr3 198022430 13869346 0.07003926777385774 0.300947936344683 chr4 191154276 7385162 0.038634563424571264 0.2333746622355313 chr5 180915260 5897576 0.03259855470456168 0.20322057703473648 chr6 171115067 8269013 0.04832428344840025 0.2813060369457127 chr7 159138663 9051145 0.056875839154184676 0.7609492190291722 chr8 146364022 7537142 0.051495865561825026 0.3364445068009787 chr9 141213431 4274353 0.030268742638226813 0.25660458635750555 chr10 135534747 6652249 0.04908150232500895 0.4020149032974954 chr11 135006516 5986179 0.044339926526213 0.3058506087374921 chr12 133851895 5501366 0.04110039682292133 0.2302164401840078 chr13 115169878 4086634 0.03548353155327646 0.21544512103616614 chr14 107349540 4959563 0.04620013276256237 0.24871902496842574 chr15 102531392 2574344 0.02510786160008439 0.1905538164588339 chr16 90354753 3592110 0.03975562857219033 0.24737988339863212 chr17 81195210 2695945 0.03320325176817696 0.21433738768135321 chr18 78077248 2856180 0.036581463526993166 0.5289832487691488 chr19 59128983 2372101 0.040117398941226505 0.4790778924462925 chr20 63025520 2437648 0.03867715807818801 0.22315858844095735 chr21 48129895 1660079 0.03449163975944681 0.22049568420695148 chr22 51304566 1172000 0.022843970651657008 0.1685748406506614 chrMT 16571 152335 9.192867056906644 5.78319847783595 chrX 155270560 7436999 0.04789703212250925 0.2724420321709887 chrY 59373566 370433 0.0062390222611860635 0.1531958057706819