BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975308.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,115,180 number of mapped reads = 4,066,898 (98.83%) number of supplementary alignments = 17,553 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,032,369 number of mapped paired reads (second in pair) = 2,034,529 number of mapped paired reads (both in pair) = 4,052,716 number of mapped paired reads (singletons) = 14,182 number of mapped bases = 368,606,913 bp number of sequenced bases = 368,394,966 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 201,973 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 64,339.0048 std insert size = 2,406,078.2972 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 52.7503 >>>>>>> ACTG content number of A's = 107,275,438 bp (29.12%) number of C's = 71,565,304 bp (19.43%) number of T's = 107,445,375 bp (29.17%) number of G's = 82,101,263 bp (22.29%) number of N's = 7,586 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,750,275 number of insertions = 61,411 mapped reads with insertion percentage = 1.47% number of deletions = 119,801 mapped reads with deletion percentage = 2.88% homopolymer indels = 45.12% >>>>>>> Coverage mean coverageData = 0.1191X std coverageData = 1.0548X There is a 7.98% of reference with a coverageData >= 1X There is a 2.49% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 34702244 0.13922630908911557 1.008412944295786 chr2 243199373 31619172 0.13001337795389792 1.418364351959072 chr3 198022430 19854578 0.10026428824249858 0.4303991015383087 chr4 191154276 23970820 0.12540038602118428 0.8743057108824568 chr5 180915260 22588434 0.12485643278516141 0.4708340959188184 chr6 171115067 28761513 0.16808287840602604 0.856979404711641 chr7 159138663 20691221 0.13002007563680487 1.0952941836833379 chr8 146364022 19002568 0.12983086786177547 0.5927612298890106 chr9 141213431 16272071 0.11523033527880219 1.5618891794789864 chr10 135534747 17942967 0.13238647208305926 2.405565602017742 chr11 135006516 13202927 0.0977947390331886 0.8705610412168056 chr12 133851895 16418503 0.12266171502465467 0.46354124831554805 chr13 115169878 12829426 0.1113956723996877 0.44615510391190283 chr14 107349540 11112855 0.10352028522898188 0.46858235749924815 chr15 102531392 10737226 0.10472135207137342 0.42392214126972017 chr16 90354753 12142368 0.13438549270341096 1.5887307553997185 chr17 81195210 7862519 0.09683476402117809 1.0298159496693917 chr18 78077248 10445864 0.13378883436055533 1.5679767677557972 chr19 59128983 5147501 0.08705546313894828 0.6963466964136305 chr20 63025520 8019398 0.1272404892494342 0.5180873418492 chr21 48129895 4717945 0.09802525021091361 0.5798575221545513 chr22 51304566 3982858 0.07763164783422981 0.39401481761720597 chrMT 16571 162012 9.776839056182487 9.61603884416424 chrX 155270560 11723364 0.07550281263879 0.5153716565718538 chrY 59373566 4696559 0.07910185148724265 1.6637666508544833