BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365376.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 686,238,352 number of mapped reads = 648,640,082 (94.52%) number of supplementary alignments = 3,161,957 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 323,892,522 number of mapped paired reads (second in pair) = 324,747,560 number of mapped paired reads (both in pair) = 646,092,110 number of mapped paired reads (singletons) = 2,547,972 number of mapped bases = 66,827,335,501 bp number of sequenced bases = 66,806,352,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 372,504,677 duplication rate = 33.04% >>>>>>> Insert size mean insert size = 79,050.3171 std insert size = 2,733,033.103 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 53.6417 >>>>>>> ACTG content number of A's = 19,830,061,427 bp (29.68%) number of C's = 13,414,613,577 bp (20.08%) number of T's = 19,231,213,695 bp (28.79%) number of G's = 14,296,096,535 bp (21.4%) number of N's = 34,366,832 bp (0.05%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 331,111,736 number of insertions = 18,010,530 mapped reads with insertion percentage = 2.71% number of deletions = 10,000,543 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.97% >>>>>>> Coverage mean coverageData = 21.5872X std coverageData = 273.3837X There is a 89.1% of reference with a coverageData >= 1X There is a 87.45% of reference with a coverageData >= 2X There is a 85.24% of reference with a coverageData >= 3X There is a 83.15% of reference with a coverageData >= 4X There is a 80.72% of reference with a coverageData >= 5X There is a 78.33% of reference with a coverageData >= 6X There is a 75.74% of reference with a coverageData >= 7X There is a 73.17% of reference with a coverageData >= 8X There is a 70.47% of reference with a coverageData >= 9X There is a 67.81% of reference with a coverageData >= 10X There is a 65.09% of reference with a coverageData >= 11X There is a 62.42% of reference with a coverageData >= 12X There is a 59.74% of reference with a coverageData >= 13X There is a 57.12% of reference with a coverageData >= 14X There is a 54.51% of reference with a coverageData >= 15X There is a 51.99% of reference with a coverageData >= 16X There is a 49.51% of reference with a coverageData >= 17X There is a 47.11% of reference with a coverageData >= 18X There is a 44.77% of reference with a coverageData >= 19X There is a 42.52% of reference with a coverageData >= 20X There is a 40.33% of reference with a coverageData >= 21X There is a 38.25% of reference with a coverageData >= 22X There is a 36.23% of reference with a coverageData >= 23X There is a 34.3% of reference with a coverageData >= 24X There is a 32.45% of reference with a coverageData >= 25X There is a 30.69% of reference with a coverageData >= 26X There is a 29% of reference with a coverageData >= 27X There is a 27.4% of reference with a coverageData >= 28X There is a 25.87% of reference with a coverageData >= 29X There is a 24.42% of reference with a coverageData >= 30X There is a 23.03% of reference with a coverageData >= 31X There is a 21.73% of reference with a coverageData >= 32X There is a 20.48% of reference with a coverageData >= 33X There is a 19.31% of reference with a coverageData >= 34X There is a 18.19% of reference with a coverageData >= 35X There is a 17.14% of reference with a coverageData >= 36X There is a 16.14% of reference with a coverageData >= 37X There is a 15.2% of reference with a coverageData >= 38X There is a 14.3% of reference with a coverageData >= 39X There is a 13.46% of reference with a coverageData >= 40X There is a 12.67% of reference with a coverageData >= 41X There is a 11.92% of reference with a coverageData >= 42X There is a 11.22% of reference with a coverageData >= 43X There is a 10.56% of reference with a coverageData >= 44X There is a 9.93% of reference with a coverageData >= 45X There is a 9.34% of reference with a coverageData >= 46X There is a 8.79% of reference with a coverageData >= 47X There is a 8.27% of reference with a coverageData >= 48X There is a 7.78% of reference with a coverageData >= 49X There is a 7.33% of reference with a coverageData >= 50X There is a 6.9% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5602133921 22.475907576575306 766.7640520052354 chr2 243199373 5826371006 23.957179387958373 166.26584069639378 chr3 198022430 4505355474 22.7517431939402 41.652147858255404 chr4 191154276 4437491559 23.21418935457138 97.52802014846677 chr5 180915260 4136189379 22.86257875095777 27.81277137874173 chr6 171115067 3961021718 23.148293060598807 114.12141000827526 chr7 159138663 3713423699 23.33451613200998 205.14332264844649 chr8 146364022 3408998414 23.291232144467852 86.65719504022142 chr9 141213431 2871847886 20.33693159116005 239.09154687738467 chr10 135534747 3521928327 25.985427390069944 478.34407177654214 chr11 135006516 3119056800 23.103009339193672 166.6782956631315 chr12 133851895 3001431386 22.423525539178957 58.410614017338155 chr13 115169878 2172398480 18.86255779484285 19.704871277087932 chr14 107349540 2038907812 18.993167665180493 28.81554654138984 chr15 102531392 1852880755 18.071350821024648 31.24629820300534 chr16 90354753 1961621832 21.710222947541013 77.26162852965264 chr17 81195210 1838384401 22.6415376104083 134.73960951393892 chr18 78077248 1878402130 24.058252283687047 298.2203493537486 chr19 59128983 1316784241 22.26969202226935 396.4466990998738 chr20 63025520 1391512450 22.07855563904907 38.718582668449464 chr21 48129895 943754876 19.608496465658195 78.29496321042274 chr22 51304566 821918305 16.020373410818834 70.1353291194699 chrMT 16571 37405129 2257.2644378733935 429.5012520057788 chrX 155270560 1834718242 11.816266019778636 70.06719098617326 chrY 59373566 633397279 10.668001295391285 204.2244942174937