BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717043.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 = 1,014,856 number of mapped reads = 905,333 (89.21%) number of supplementary alignments = 25,080 (2.47%) number of secondary alignments = 0 number of mapped bases = 66,015,889 bp number of sequenced bases = 65,994,110 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,566 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2923 >>>>>>> ACTG content number of A's = 17,386,885 bp (26.35%) number of C's = 13,763,370 bp (20.86%) number of T's = 19,440,014 bp (29.46%) number of G's = 15,395,765 bp (23.33%) number of N's = 8,076 bp (0.01%) GC percentage = 44.18% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 480,645 number of insertions = 5,757 mapped reads with insertion percentage = 0.63% number of deletions = 12,682 mapped reads with deletion percentage = 1.38% homopolymer indels = 39.66% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.2047X There is a 1.96% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 6181717 0.0248012100238659 0.22563700107162285 chr2 243199373 5399851 0.022203391947067233 0.3360149312189583 chr3 198022430 5344906 0.026991417083408176 0.17785389774273752 chr4 191154276 2695642 0.014101918389730397 0.13087832050702142 chr5 180915260 3898149 0.021546822528956375 0.15761362814736202 chr6 171115067 4802679 0.028066955670244982 0.1888222476166328 chr7 159138663 3103139 0.01949959200046817 0.24676678050363152 chr8 146364022 4247677 0.029021319187306837 0.27258098489097043 chr9 141213431 3435682 0.024329711243968006 0.21123446366766735 chr10 135534747 3536588 0.02609358912220495 0.20589953994024343 chr11 135006516 3265669 0.02418897321963334 0.18483253636355337 chr12 133851895 2388736 0.017846112675506013 0.14235116624560798 chr13 115169878 2002626 0.017388452907799383 0.1391251276075421 chr14 107349540 1372859 0.012788680789875764 0.1282929485243953 chr15 102531392 1337073 0.013040620769100647 0.12125293238302072 chr16 90354753 1738602 0.019241953989957785 0.1538780384777729 chr17 81195210 2091822 0.025762874435573232 0.1799529320498422 chr18 78077248 2060644 0.02639237489518073 0.3255193655856888 chr19 59128983 1277609 0.021607153297393936 0.22913715824842748 chr20 63025520 1213697 0.019257231039109236 0.15609289033481172 chr21 48129895 1200758 0.02494827798814022 0.17321244061747143 chr22 51304566 987865 0.019254913880374702 0.14896597017013208 chrMT 16571 15913 0.9602920765192203 1.2672417357222154 chrX 155270560 2279469 0.014680625870094112 0.14534303903284118 chrY 59373566 136517 0.0022992892156755416 0.06615577475501282