BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617698.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 43,081,624 number of mapped reads = 42,322,187 (98.24%) number of supplementary alignments = 1,636,752 (3.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,340,962 number of mapped paired reads (second in pair) = 20,981,225 number of mapped paired reads (both in pair) = 41,843,678 number of mapped paired reads (singletons) = 478,509 number of mapped bases = 5,614,464,702 bp number of sequenced bases = 5,610,251,626 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,342,832 duplication rate = 23.4% >>>>>>> Insert size mean insert size = 270,608.3221 std insert size = 5,088,590.6981 median insert size = 259 >>>>>>> Mapping quality mean mapping quality = 53.1437 >>>>>>> ACTG content number of A's = 1,611,963,814 bp (28.73%) number of C's = 1,070,489,202 bp (19.08%) number of T's = 1,663,602,093 bp (29.65%) number of G's = 1,263,982,486 bp (22.53%) number of N's = 214,031 bp (0%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 61,360,465 number of insertions = 972,611 mapped reads with insertion percentage = 2.17% number of deletions = 2,194,310 mapped reads with deletion percentage = 4.98% homopolymer indels = 46.44% >>>>>>> Coverage mean coverageData = 1.8136X std coverageData = 14.8945X There is a 42.08% of reference with a coverageData >= 1X There is a 29.72% of reference with a coverageData >= 2X There is a 21.46% of reference with a coverageData >= 3X There is a 16.19% of reference with a coverageData >= 4X There is a 12.34% of reference with a coverageData >= 5X There is a 9.6% of reference with a coverageData >= 6X There is a 7.55% of reference with a coverageData >= 7X There is a 6% of reference with a coverageData >= 8X There is a 4.82% of reference with a coverageData >= 9X There is a 3.9% of reference with a coverageData >= 10X There is a 3.19% of reference with a coverageData >= 11X There is a 2.62% of reference with a coverageData >= 12X There is a 2.16% of reference with a coverageData >= 13X There is a 1.8% of reference with a coverageData >= 14X There is a 1.51% of reference with a coverageData >= 15X There is a 1.27% of reference with a coverageData >= 16X There is a 1.07% of reference with a coverageData >= 17X There is a 0.91% of reference with a coverageData >= 18X There is a 0.77% of reference with a coverageData >= 19X There is a 0.66% of reference with a coverageData >= 20X There is a 0.57% of reference with a coverageData >= 21X There is a 0.49% of reference with a coverageData >= 22X There is a 0.43% of reference with a coverageData >= 23X There is a 0.37% of reference with a coverageData >= 24X There is a 0.33% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 510826834 2.049450596955584 17.42580644912138 chr2 243199373 546972885 2.2490719373688517 21.485405045820702 chr3 198022430 333706936 1.6851976616992328 3.531191306142784 chr4 191154276 403118892 2.108866725011163 11.890468855811541 chr5 180915260 251824962 1.3919498111989006 3.3109028731895505 chr6 171115067 380296573 2.2224610589083893 13.22772252542975 chr7 159138663 341303137 2.1446902378462234 17.11051730404063 chr8 146364022 350070559 2.3917801261296305 7.2764360932953105 chr9 141213431 207365662 1.4684556598585867 28.67473941469782 chr10 135534747 244834978 1.8064369722105285 29.023868450646123 chr11 135006516 193721743 1.4349066159147459 10.430640398579648 chr12 133851895 241692724 1.8056727848343126 8.38222801472216 chr13 115169878 114747204 0.996329995244069 2.4311382654041074 chr14 107349540 296601500 2.76295082400912 5.294853746379025 chr15 102531392 109061666 1.0636904841787382 4.289565028215152 chr16 90354753 153786262 1.7020273631869705 14.788662472588765 chr17 81195210 154796208 1.9064697043089118 17.79830455507553 chr18 78077248 167480282 2.1450587244058603 24.70350955671637 chr19 59128983 105814203 1.7895488410480525 8.885334695037493 chr20 63025520 153958082 2.4427895557228245 5.614477522300282 chr21 48129895 75903603 1.5770573154169565 6.339183127510036 chr22 51304566 52978252 1.0326225544915437 3.185275238122174 chrMT 16571 8317744 501.9458089433347 241.24274311088078 chrX 155270560 199236027 1.2831539153333382 4.745702475657173 chrY 59373566 16047784 0.2702849951778204 13.933020220758799