BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472636.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,872,540 number of mapped reads = 13,765,028 (99.23%) number of supplementary alignments = 67,364 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,900,344 number of mapped paired reads (second in pair) = 6,864,684 number of mapped paired reads (both in pair) = 13,692,904 number of mapped paired reads (singletons) = 72,124 number of mapped bases = 1,354,408,182 bp number of sequenced bases = 1,354,244,507 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,094,072 duplication rate = 48.16% >>>>>>> Insert size mean insert size = 21,576.0506 std insert size = 1,445,607.3435 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 54.7953 >>>>>>> ACTG content number of A's = 363,493,921 bp (26.84%) number of C's = 315,228,206 bp (23.28%) number of T's = 364,543,743 bp (26.92%) number of G's = 310,731,528 bp (22.95%) number of N's = 247,109 bp (0.02%) GC percentage = 46.22% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 8,261,380 number of insertions = 77,312 mapped reads with insertion percentage = 0.56% number of deletions = 67,917 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 0.4375X std coverageData = 19.1518X There is a 2.9% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 194448866 0.7801339279311164 32.622544307157625 chr2 243199373 106509242 0.43795031494591885 16.55771640685174 chr3 198022430 96385380 0.4867397092339489 14.844166578204163 chr4 191154276 29473930 0.15418922671653967 9.013517216293371 chr5 180915260 51529589 0.28482721136956607 16.337134140707466 chr6 171115067 135244722 0.7903729599685105 24.349422147477235 chr7 159138663 76851967 0.4829245486371844 24.080695983248315 chr8 146364022 81628597 0.5577094417369864 20.179311699949775 chr9 141213431 54816305 0.38818053362077154 10.79357772774363 chr10 135534747 20515549 0.15136744970645793 11.462606991684535 chr11 135006516 48049486 0.3559049401734061 15.569286694090291 chr12 133851895 37428741 0.2796280246910214 10.985034159084021 chr13 115169878 40066267 0.3478884209636829 12.829485528467178 chr14 107349540 25048966 0.2333402267024153 13.39066459047619 chr15 102531392 21320497 0.20794116400955523 8.858227371197865 chr16 90354753 84960000 0.9402936445413115 40.04270385789914 chr17 81195210 54833515 0.6753294313790186 22.279574526300248 chr18 78077248 14206847 0.1819588595130812 7.255681073839626 chr19 59128983 25481193 0.43094252103067626 12.286373937532472 chr20 63025520 82879148 1.3150093485940297 35.225584739480595 chr21 48129895 9730013 0.20216152559651335 10.686972737250287 chr22 51304566 11561881 0.22535773911429247 10.377026566575813 chrMT 16571 2996 0.1807977792529117 0.5422430350901265 chrX 155270560 50111462 0.3227364028312901 12.82999260010135 chrY 59373566 1323023 0.02228303080195655 1.6462328642750212