BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867862.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 = 22,016,942 number of mapped reads = 21,626,266 (98.23%) number of supplementary alignments = 90,343 (0.41%) number of secondary alignments = 0 number of mapped bases = 1,895,972,920 bp number of sequenced bases = 1,895,424,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,424,829 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.8365 >>>>>>> ACTG content number of A's = 515,397,412 bp (27.19%) number of C's = 421,759,195 bp (22.25%) number of T's = 524,699,085 bp (27.68%) number of G's = 433,168,211 bp (22.85%) number of N's = 400,220 bp (0.02%) GC percentage = 45.1% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 9,499,387 number of insertions = 213,732 mapped reads with insertion percentage = 0.96% number of deletions = 199,237 mapped reads with deletion percentage = 0.89% homopolymer indels = 33.19% >>>>>>> Coverage mean coverageData = 0.6125X std coverageData = 8.6901X There is a 38.9% of reference with a coverageData >= 1X There is a 12.77% of reference with a coverageData >= 2X There is a 3.83% of reference with a coverageData >= 3X There is a 1.2% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 154855517 0.621284377863195 15.384802155648583 chr2 243199373 141055920 0.5800011663681386 5.652042728412785 chr3 198022430 103748386 0.5239223960639207 5.338779801086057 chr4 191154276 117148691 0.6128489168612686 8.633355415761605 chr5 180915260 98569237 0.5448364996960455 0.9345204197093537 chr6 171115067 93557300 0.5467508013189745 1.8241403232113478 chr7 159138663 107285826 0.6741656865622907 4.173346275162507 chr8 146364022 81335321 0.5557056979480928 2.316221544860131 chr9 141213431 84284889 0.5968617036151469 3.3983432693563453 chr10 135534747 103093204 0.7606403987311091 28.528049755453885 chr11 135006516 76113492 0.5637764328352862 1.9697784509589298 chr12 133851895 111516117 0.8331306553411142 1.5191038668434678 chr13 115169878 61941614 0.5378282505430804 0.8703335211653523 chr14 107349540 61520039 0.5730815334653506 1.2130004811143191 chr15 102531392 50526003 0.49278569240530745 0.8210282607381151 chr16 90354753 76009221 0.8412310196896892 9.270898579922795 chr17 81195210 63756953 0.78523047110784 1.9965498620096969 chr18 78077248 52504937 0.672474227062921 8.571392149856859 chr19 59128983 42935031 0.7261249698815215 9.47473368199668 chr20 63025520 53336897 0.8462746043190124 2.6271341462560693 chr21 48129895 27384005 0.5689604143121443 6.388371192540197 chr22 51304566 28457367 0.5546751335933726 1.0459091852065467 chrMT 16571 2554042 154.12721018647034 71.63836370307 chrX 155270560 90801844 0.5847975559565187 1.5903153888663832 chrY 59373566 11681067 0.19673851154569358 11.059614767862383