BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927010.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 28,366,694 number of mapped reads = 27,576,626 (97.21%) number of supplementary alignments = 567,632 (2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,836,666 number of mapped paired reads (second in pair) = 13,739,960 number of mapped paired reads (both in pair) = 27,138,916 number of mapped paired reads (singletons) = 437,710 number of mapped bases = 2,521,112,569 bp number of sequenced bases = 2,519,120,871 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,082,472 duplication rate = 8.08% >>>>>>> Insert size mean insert size = 232,921.6267 std insert size = 4,833,025.7733 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 48.9087 >>>>>>> ACTG content number of A's = 721,119,661 bp (28.63%) number of C's = 487,321,062 bp (19.34%) number of T's = 737,235,215 bp (29.27%) number of G's = 572,979,679 bp (22.75%) number of N's = 465,254 bp (0.02%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 24,434,893 number of insertions = 434,156 mapped reads with insertion percentage = 1.54% number of deletions = 1,371,761 mapped reads with deletion percentage = 4.84% homopolymer indels = 52.08% >>>>>>> Coverage mean coverageData = 0.8144X std coverageData = 5.0225X There is a 30.01% of reference with a coverageData >= 1X There is a 17.4% of reference with a coverageData >= 2X There is a 10.51% of reference with a coverageData >= 3X There is a 6.7% of reference with a coverageData >= 4X There is a 4.4% of reference with a coverageData >= 5X There is a 2.97% of reference with a coverageData >= 6X There is a 2.04% of reference with a coverageData >= 7X There is a 1.43% of reference with a coverageData >= 8X There is a 1.02% of reference with a coverageData >= 9X There is a 0.73% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 252072339 1.0113208062980112 4.8759489533168505 chr2 243199373 262318509 1.078615071100533 7.051508998162826 chr3 198022430 198126926 1.0005276977966586 1.9794847941003655 chr4 191154276 176988111 0.9258914563857311 2.675499929341075 chr5 180915260 177948306 0.9836003109964301 1.9822190260854362 chr6 171115067 3712284 0.021694664678476267 0.4336148926127302 chr7 159138663 4187811 0.026315484377294286 0.8686087979401821 chr8 146364022 147119158 1.0051593006920785 2.388534916295079 chr9 141213431 125141860 0.8861895013371639 3.9602736425375746 chr10 135534747 141690317 1.045416914379897 7.450123789826818 chr11 135006516 141721779 1.0497402880909836 3.1953221564655894 chr12 133851895 136533863 1.0200368325005784 2.090043926121007 chr13 115169878 88619618 0.7694687147276478 1.7203128847488958 chr14 107349540 90503879 0.8430765422935208 1.9446691638520859 chr15 102531392 1841383 0.01795921194554737 0.33245629526672565 chr16 90354753 93800630 1.0381371968334638 5.210119787056124 chr17 81195210 1881560 0.02317328817796025 0.8103806115040203 chr18 78077248 75992783 0.9733025298227724 3.443876067064933 chr19 59128983 59555977 1.0072213993601074 3.426224397632364 chr20 63025520 73362119 1.1640065643250543 2.3544216889068377 chr21 48129895 39736709 0.8256138726253195 3.7250618559005018 chr22 51304566 41796031 0.8146649364502957 2.0926378183866827 chrMT 16571 18786000 1133.6672500150867 963.1362150871729 chrX 155270560 163315151 1.0518101499730534 2.4183975967000735 chrY 59373566 4359466 0.07342435857735073 2.728518844865566