BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717088.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 = 1,540,019 number of mapped reads = 1,394,636 (90.56%) number of supplementary alignments = 21,910 (1.42%) number of secondary alignments = 0 number of mapped bases = 110,147,866 bp number of sequenced bases = 110,099,328 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,117 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2263 >>>>>>> ACTG content number of A's = 26,627,943 bp (24.19%) number of C's = 20,576,375 bp (18.69%) number of T's = 34,976,483 bp (31.77%) number of G's = 27,911,447 bp (25.35%) number of N's = 7,080 bp (0.01%) GC percentage = 44.04% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 905,989 number of insertions = 10,295 mapped reads with insertion percentage = 0.73% number of deletions = 27,784 mapped reads with deletion percentage = 1.96% homopolymer indels = 44.03% >>>>>>> Coverage mean coverageData = 0.0356X std coverageData = 0.4339X There is a 3.09% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 8885028 0.0356469643459785 0.6843144102235889 chr2 243199373 9339473 0.03840253732890997 0.6377981444022363 chr3 198022430 7105517 0.03588238463693229 0.21395465663386073 chr4 191154276 6956014 0.03638952863392917 0.23567843632445526 chr5 180915260 6591526 0.036434328425363344 0.2213908247463632 chr6 171115067 6369664 0.03722444850516875 0.265731577995936 chr7 159138663 6182804 0.03885167742046444 0.5630497059056527 chr8 146364022 5638799 0.03852585439336998 0.590432622158352 chr9 141213431 4742279 0.03358235095923701 0.4872056851339183 chr10 135534747 5270763 0.0388886474993752 0.4298964904362807 chr11 135006516 4982047 0.036902270702252625 0.42516617553221625 chr12 133851895 4977700 0.03718811750853434 0.22219139480115938 chr13 115169878 3352134 0.02910599592716422 0.18786951201270133 chr14 107349540 3300850 0.03074861801922952 0.27036802699232737 chr15 102531392 3136843 0.030593976525745404 0.19953544210942933 chr16 90354753 3260686 0.036087597959567216 0.25563433621029014 chr17 81195210 3086449 0.03801269803969963 0.24153573877694284 chr18 78077248 3052142 0.03909131121014921 0.9359210280145019 chr19 59128983 2407971 0.040724038835574086 0.499255940416103 chr20 63025520 2217854 0.03518977709346944 0.22435401855068968 chr21 48129895 1411133 0.029319261968055406 0.20896405086834055 chr22 51304566 1249237 0.024349431198774783 0.173620722872882 chrMT 16571 2569 0.155029871462193 0.3922825544885534 chrX 155270560 6326759 0.04074667470768444 0.3355350804089339 chrY 59373566 301625 0.005080122692984282 0.14914501435867092