BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716223.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 = 1,122,279 number of mapped reads = 1,010,151 (90.01%) number of supplementary alignments = 3,645 (0.32%) number of secondary alignments = 0 number of mapped bases = 58,763,646 bp number of sequenced bases = 58,744,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,143 duplication rate = 1.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5804 >>>>>>> ACTG content number of A's = 15,057,813 bp (25.63%) number of C's = 11,350,358 bp (19.32%) number of T's = 17,649,805 bp (30.05%) number of G's = 14,685,939 bp (25%) number of N's = 450 bp (0%) GC percentage = 44.32% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 301,595 number of insertions = 4,389 mapped reads with insertion percentage = 0.43% number of deletions = 11,727 mapped reads with deletion percentage = 1.15% homopolymer indels = 40.2% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.1783X There is a 1.75% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% 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 4725447 0.018958616757067177 0.2257750696924524 chr2 243199373 4948414 0.020347149496968482 0.23825667322059002 chr3 198022430 3910974 0.01975015658579687 0.1505153857614367 chr4 191154276 3738989 0.019560059435970976 0.161610597273616 chr5 180915260 3475980 0.019213304615652654 0.14721407344161067 chr6 171115067 3348450 0.019568411237567994 0.1622761643342886 chr7 159138663 3245553 0.020394497093393325 0.21127200598414853 chr8 146364022 2914131 0.019910159342300664 0.18657458464874221 chr9 141213431 2466177 0.01746418157632612 0.16020702140165874 chr10 135534747 2858119 0.021087721512476797 0.2151773128501048 chr11 135006516 2637821 0.019538471757911298 0.16613499980644028 chr12 133851895 2643983 0.019753048696098025 0.15080285522177897 chr13 115169878 1844421 0.016014786435737997 0.1352707594937495 chr14 107349540 1773370 0.01651958639040279 0.13937267236033607 chr15 102531392 1699775 0.016578093468193625 0.13822879705767796 chr16 90354753 1771272 0.019603528770644748 0.15797563310217458 chr17 81195210 1661492 0.020462931249269508 0.15557143756046793 chr18 78077248 1542003 0.019749709928300753 0.23344637705036975 chr19 59128983 1290910 0.021832102202738714 0.20013539514669917 chr20 63025520 1276805 0.020258539715340706 0.1544036755099021 chr21 48129895 766464 0.01592490488499923 0.14498458471799539 chr22 51304566 744583 0.014512996757442602 0.1286274780989463 chrMT 16571 5028 0.30342164021483314 0.5800789878502144 chrX 155270560 3288125 0.021176744644960385 0.1622130042606543 chrY 59373566 185360 0.003121928031070258 0.10355030520386237