BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238605.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 = 3,656,271 number of mapped reads = 2,690,461 (73.58%) number of supplementary alignments = 24,341 (0.67%) number of secondary alignments = 0 number of mapped bases = 161,517,123 bp number of sequenced bases = 161,442,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,394,998 duplication rate = 23.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.4325 >>>>>>> ACTG content number of A's = 40,840,891 bp (25.3%) number of C's = 27,517,834 bp (17.04%) number of T's = 55,003,994 bp (34.07%) number of G's = 38,076,072 bp (23.58%) number of N's = 3,708 bp (0%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,030,863 number of insertions = 11,568 mapped reads with insertion percentage = 0.43% number of deletions = 43,817 mapped reads with deletion percentage = 1.61% homopolymer indels = 40.94% >>>>>>> Coverage mean coverageData = 0.0522X std coverageData = 1.5239X There is a 0.88% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 6637050 0.02662801790973271 1.6721126019711994 chr2 243199373 18252364 0.07505103230673214 1.9532002078677957 chr3 198022430 7569821 0.038227088719192066 0.8695402278118545 chr4 191154276 12428519 0.06501826304947528 1.1147873024373773 chr5 180915260 9886999 0.054649889677631396 1.0167372107291932 chr6 171115067 14741764 0.08615117451930752 1.5614345068368478 chr7 159138663 2795329 0.017565366877563878 0.8151665254187178 chr8 146364022 11784841 0.08051733505929483 2.1392129166204774 chr9 141213431 2244598 0.01589507445647999 0.6603005735543336 chr10 135534747 2106997 0.015545806862353902 0.7340252117501771 chr11 135006516 2735577 0.020262555327329533 0.7305577783333321 chr12 133851895 8547993 0.06386157625934247 1.1241412951146106 chr13 115169878 8561278 0.07433608638536546 1.4203976325510892 chr14 107349540 7169558 0.06678703979541971 1.3494533317993311 chr15 102531392 3323991 0.032419251657092495 0.9827483097846147 chr16 90354753 4649996 0.051463767489907254 1.011039795900555 chr17 81195210 2266772 0.027917558190932692 0.6892609155108415 chr18 78077248 2684049 0.034376839204168674 5.047485492089532 chr19 59128983 6451123 0.10910255297304877 1.872006393500386 chr20 63025520 8662354 0.1374420076185012 1.7062345747541146 chr21 48129895 4091565 0.08501088564602105 1.278349987160952 chr22 51304566 3702126 0.0721597761883416 1.1220628633660918 chrMT 16571 14971 0.9034457787701407 3.647208975343941 chrX 155270560 9534625 0.06140652162264373 1.1393851637452774 chrY 59373566 672863 0.01133270317635966 0.7849163425764581