BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068080.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 = 2,520,027 number of mapped reads = 2,280,656 (90.5%) number of supplementary alignments = 19,926 (0.79%) number of secondary alignments = 0 number of mapped bases = 151,954,703 bp number of sequenced bases = 151,887,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,060 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7506 >>>>>>> ACTG content number of A's = 42,707,133 bp (28.12%) number of C's = 27,707,678 bp (18.24%) number of T's = 48,468,498 bp (31.91%) number of G's = 33,001,025 bp (21.73%) number of N's = 3,203 bp (0%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,185,102 number of insertions = 11,752 mapped reads with insertion percentage = 0.51% number of deletions = 41,607 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 0.5131X There is a 4.11% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.09% 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% 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 12851952 0.05156236702014074 0.940185423496963 chr2 243199373 15511970 0.06378293582196036 0.5549747604281154 chr3 198022430 11095390 0.05603097588490354 0.27171796378250573 chr4 191154276 10869086 0.056860281796678194 0.2863212680443901 chr5 180915260 8463833 0.04678341119483232 0.251030311749031 chr6 171115067 9661657 0.05646292386397511 0.30960721168869487 chr7 159138663 14201414 0.08923924414270089 0.742156072892358 chr8 146364022 5578735 0.038115480319336946 1.0995226365689206 chr9 141213431 3464166 0.024531420102667147 0.4000483457772054 chr10 135534747 8609773 0.06352447022312294 0.35871024194871004 chr11 135006516 7046966 0.05219722876190657 0.39103698012624355 chr12 133851895 5188782 0.03876509929127264 0.2528197575841016 chr13 115169878 3943819 0.03424349377186976 0.21285530792115134 chr14 107349540 720513 0.006711840591026286 0.17535374579338953 chr15 102531392 2869116 0.027982805500192564 0.20002640953659126 chr16 90354753 3672072 0.0406406069197046 0.2586431352761019 chr17 81195210 4615634 0.05684613661323125 0.3011792058629469 chr18 78077248 4622927 0.05920965605754957 0.7602990432305878 chr19 59128983 2285138 0.038646665037347254 0.6686565276979751 chr20 63025520 2212239 0.03510068619822573 0.2536271325605654 chr21 48129895 3534019 0.07342669249538152 0.3200770855265321 chr22 51304566 1147059 0.022357834583378016 0.16715224162112857 chrMT 16571 30874 1.8631343914066743 1.862894150421124 chrX 155270560 9469790 0.06098896017377666 0.339534708415809 chrY 59373566 287779 0.004846921271328052 0.1110472737319633