BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524504.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 = 1,414,774 number of mapped reads = 1,315,372 (92.97%) number of supplementary alignments = 3,067 (0.22%) number of secondary alignments = 0 number of mapped bases = 77,319,288 bp number of sequenced bases = 77,294,562 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,430 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6606 >>>>>>> ACTG content number of A's = 18,785,998 bp (24.3%) number of C's = 15,057,786 bp (19.48%) number of T's = 23,983,804 bp (31.03%) number of G's = 19,465,335 bp (25.18%) number of N's = 1,639 bp (0%) GC percentage = 44.66% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 359,801 number of insertions = 4,051 mapped reads with insertion percentage = 0.31% number of deletions = 14,246 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.42% >>>>>>> Coverage mean coverageData = 0.025X std coverageData = 0.2425X There is a 2.24% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7734189 0.03102976822673593 0.4458132051281902 chr2 243199373 6108126 0.025115714422503876 0.2559532857860669 chr3 198022430 4282966 0.02162869125482401 0.16196200193060617 chr4 191154276 4342077 0.022715039866542143 0.18295611804191392 chr5 180915260 4297657 0.023755082904559847 0.16791642566005152 chr6 171115067 3355225 0.019608004478062706 0.19091228255697504 chr7 159138663 3834449 0.024095018317453126 0.31279286564820624 chr8 146364022 7180924 0.04906208439666956 0.276218238080119 chr9 141213431 3252215 0.023030493466304914 0.21404971492164968 chr10 135534747 4063330 0.029979987345975567 0.25933630220008347 chr11 135006516 2603152 0.019281676745143174 0.2140398212250299 chr12 133851895 3560090 0.026597232710078553 0.17758928504711113 chr13 115169878 1708943 0.014838454547985195 0.13442734738527323 chr14 107349540 1837914 0.017120837220168807 0.14711849492730353 chr15 102531392 2053480 0.020027817431757876 0.1590782801353821 chr16 90354753 2388723 0.02643715931579161 0.1886372727472514 chr17 81195210 2604470 0.03207664590066335 0.2061595314942079 chr18 78077248 1820742 0.023319751228936758 0.3449278983373539 chr19 59128983 1503695 0.025430760410677114 0.30179341003254245 chr20 63025520 2179804 0.03458605339551343 0.2051556422902358 chr21 48129895 1059611 0.022015651602813595 0.17293963199381765 chr22 51304566 611223 0.011913617980902519 0.11748629868474847 chrMT 16571 5655 0.3412588256592843 0.6537923304651851 chrX 155270560 4676520 0.03011852343419126 0.2085460214564316 chrY 59373566 254108 0.004279817048549854 0.11875694622937147