BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617727.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 = 48,253,518 number of mapped reads = 47,588,589 (98.62%) number of supplementary alignments = 1,095,710 (2.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,953,276 number of mapped paired reads (second in pair) = 23,635,313 number of mapped paired reads (both in pair) = 47,194,988 number of mapped paired reads (singletons) = 393,601 number of mapped bases = 6,352,064,096 bp number of sequenced bases = 6,347,444,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,227,230 duplication rate = 24.05% >>>>>>> Insert size mean insert size = 132,554.7402 std insert size = 3,537,906.1155 median insert size = 268 >>>>>>> Mapping quality mean mapping quality = 53.5153 >>>>>>> ACTG content number of A's = 1,838,772,122 bp (28.97%) number of C's = 1,204,282,332 bp (18.97%) number of T's = 1,895,071,558 bp (29.86%) number of G's = 1,409,073,001 bp (22.2%) number of N's = 245,110 bp (0%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 75,623,799 number of insertions = 1,094,936 mapped reads with insertion percentage = 2.17% number of deletions = 2,389,961 mapped reads with deletion percentage = 4.83% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 2.0519X std coverageData = 22.5248X There is a 35.28% of reference with a coverageData >= 1X There is a 26.45% of reference with a coverageData >= 2X There is a 20.45% of reference with a coverageData >= 3X There is a 16.4% of reference with a coverageData >= 4X There is a 13.32% of reference with a coverageData >= 5X There is a 11% of reference with a coverageData >= 6X There is a 9.17% of reference with a coverageData >= 7X There is a 7.71% of reference with a coverageData >= 8X There is a 6.54% of reference with a coverageData >= 9X There is a 5.58% of reference with a coverageData >= 10X There is a 4.78% of reference with a coverageData >= 11X There is a 4.13% of reference with a coverageData >= 12X There is a 3.57% of reference with a coverageData >= 13X There is a 3.11% of reference with a coverageData >= 14X There is a 2.71% of reference with a coverageData >= 15X There is a 2.37% of reference with a coverageData >= 16X There is a 2.09% of reference with a coverageData >= 17X There is a 1.84% of reference with a coverageData >= 18X There is a 1.62% of reference with a coverageData >= 19X There is a 1.44% of reference with a coverageData >= 20X There is a 1.28% of reference with a coverageData >= 21X There is a 1.14% of reference with a coverageData >= 22X There is a 1.02% of reference with a coverageData >= 23X There is a 0.91% of reference with a coverageData >= 24X There is a 0.82% of reference with a coverageData >= 25X There is a 0.73% of reference with a coverageData >= 26X There is a 0.66% of reference with a coverageData >= 27X There is a 0.6% of reference with a coverageData >= 28X There is a 0.54% of reference with a coverageData >= 29X There is a 0.49% of reference with a coverageData >= 30X There is a 0.44% of reference with a coverageData >= 31X There is a 0.4% of reference with a coverageData >= 32X There is a 0.37% of reference with a coverageData >= 33X There is a 0.33% of reference with a coverageData >= 34X There is a 0.31% of reference with a coverageData >= 35X There is a 0.28% of reference with a coverageData >= 36X There is a 0.26% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 587386750 2.356610979115675 19.016478256183472 chr2 243199373 585281052 2.4065894775148124 24.546189362694015 chr3 198022430 314076643 1.586065997675112 4.2158666052224545 chr4 191154276 310659077 1.6251746155027158 19.912566366832944 chr5 180915260 418664193 2.314145268895504 5.400212056527323 chr6 171115067 451254415 2.6371401590252717 12.901992366508285 chr7 159138663 355049126 2.231067669583224 23.62584581993524 chr8 146364022 343878797 2.34947627361593 7.852734013841915 chr9 141213431 286879156 2.0315288281608286 42.11717037196294 chr10 135534747 359108940 2.6495710358318667 47.88009056862201 chr11 135006516 265461691 1.966287990129306 17.117335060316247 chr12 133851895 288017921 2.151765733312928 9.1389155902141 chr13 115169878 127556025 1.1075467580160152 3.397270075881371 chr14 107349540 191346378 1.7824610892603732 5.025337808609007 chr15 102531392 192823300 1.8806269595949696 6.154873323478533 chr16 90354753 266639689 2.951031131699292 43.06080956395325 chr17 81195210 143326265 1.7652059154721074 27.30919835737927 chr18 78077248 132546332 1.6976306849339773 38.25091700653811 chr19 59128983 89129953 1.5073818029307218 10.455988365776134 chr20 63025520 147604789 2.3419844691483704 7.69809048330006 chr21 48129895 83461466 1.7340878470646985 9.793759772113841 chr22 51304566 96020089 1.8715700470012746 5.884596468475151 chrMT 16571 4043409 244.00512944300283 133.96002317980683 chrX 155270560 194980355 1.2557458091218323 6.61392316557254 chrY 59373566 116868285 1.968355496787914 47.791447195919474