BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472652.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 = 13,377,654 number of mapped reads = 13,247,668 (99.03%) number of supplementary alignments = 20,218 (0.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,661,075 number of mapped paired reads (second in pair) = 6,586,593 number of mapped paired reads (both in pair) = 13,167,680 number of mapped paired reads (singletons) = 79,988 number of mapped bases = 1,302,560,626 bp number of sequenced bases = 1,302,396,041 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,853,470 duplication rate = 44.72% >>>>>>> Insert size mean insert size = 19,751.5664 std insert size = 1,424,336.9589 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 54.9315 >>>>>>> ACTG content number of A's = 357,832,781 bp (27.47%) number of C's = 293,515,629 bp (22.54%) number of T's = 362,794,498 bp (27.86%) number of G's = 287,960,846 bp (22.11%) number of N's = 292,287 bp (0.02%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 5,945,490 number of insertions = 54,833 mapped reads with insertion percentage = 0.41% number of deletions = 67,133 mapped reads with deletion percentage = 0.5% homopolymer indels = 44.29% >>>>>>> Coverage mean coverageData = 0.4208X std coverageData = 9.0622X There is a 3.11% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.5% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.45% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.4% of reference with a coverageData >= 14X There is a 0.39% of reference with a coverageData >= 15X There is a 0.38% of reference with a coverageData >= 16X There is a 0.38% of reference with a coverageData >= 17X There is a 0.37% of reference with a coverageData >= 18X There is a 0.36% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.35% of reference with a coverageData >= 21X There is a 0.34% of reference with a coverageData >= 22X There is a 0.33% of reference with a coverageData >= 23X There is a 0.33% of reference with a coverageData >= 24X There is a 0.32% of reference with a coverageData >= 25X There is a 0.31% of reference with a coverageData >= 26X There is a 0.31% of reference with a coverageData >= 27X There is a 0.3% of reference with a coverageData >= 28X There is a 0.3% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.29% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.28% of reference with a coverageData >= 33X There is a 0.27% of reference with a coverageData >= 34X There is a 0.27% of reference with a coverageData >= 35X There is a 0.26% of reference with a coverageData >= 36X There is a 0.26% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.25% of reference with a coverageData >= 40X There is a 0.24% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.24% of reference with a coverageData >= 43X There is a 0.23% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.23% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 152965347 0.6137009664661979 11.777458453431601 chr2 243199373 96655974 0.3974351282558611 9.34916943772778 chr3 198022430 116734185 0.5894998107032623 9.842653946883553 chr4 191154276 49844461 0.2607551452314883 7.582597949017673 chr5 180915260 65210221 0.36044621664308474 8.246795822865645 chr6 171115067 96069140 0.5614300463675709 10.088906494627782 chr7 159138663 79888608 0.5020062786376432 11.258926128168266 chr8 146364022 76882707 0.5252841917667445 10.478481840162424 chr9 141213431 63195610 0.4475184092085405 8.223403626542627 chr10 135534747 33536255 0.24743658539459257 6.47130972344673 chr11 135006516 50457909 0.3737442494997797 8.69009403941986 chr12 133851895 57127523 0.4267965201389192 7.616724226537867 chr13 115169878 33325510 0.28935960147496204 8.127481951492653 chr14 107349540 35354880 0.32934356309305096 7.701470837670728 chr15 102531392 27378933 0.2670297600173028 6.250815768312449 chr16 90354753 65074696 0.7202133129620751 14.474764839535444 chr17 81195210 59886968 0.73756774568352 11.926322795268927 chr18 78077248 21138921 0.27074367426474866 6.1584887842047005 chr19 59128983 28489994 0.4818279049379219 7.020451368494611 chr20 63025520 25269651 0.40094315762884625 8.24740581836054 chr21 48129895 10736641 0.22307634371527302 9.96637638032298 chr22 51304566 18665200 0.363811673214427 7.728029006876267 chrMT 16571 625964 37.774666586204816 11.997900411626462 chrX 155270560 36048251 0.23216410760674785 3.9540869387990503 chrY 59373566 1997077 0.033635793410151583 1.168887288385685