BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153320.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 148,528,930 number of mapped reads = 146,292,189 (98.49%) number of supplementary alignments = 640,379 (0.43%) number of secondary alignments = 0 number of mapped bases = 14,399,283,097 bp number of sequenced bases = 14,397,078,903 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,909,378 duplication rate = 36.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.194 >>>>>>> ACTG content number of A's = 3,773,304,930 bp (26.21%) number of C's = 3,421,536,158 bp (23.77%) number of T's = 3,812,475,687 bp (26.48%) number of G's = 3,387,016,487 bp (23.53%) number of N's = 2,745,641 bp (0.02%) GC percentage = 47.29% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 52,281,645 number of insertions = 754,162 mapped reads with insertion percentage = 0.51% number of deletions = 1,010,715 mapped reads with deletion percentage = 0.68% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 4.6514X std coverageData = 38.1727X There is a 51.91% of reference with a coverageData >= 1X There is a 33.8% of reference with a coverageData >= 2X There is a 21.64% of reference with a coverageData >= 3X There is a 14.93% of reference with a coverageData >= 4X There is a 10.86% of reference with a coverageData >= 5X There is a 8.47% of reference with a coverageData >= 6X There is a 6.99% of reference with a coverageData >= 7X There is a 6.04% of reference with a coverageData >= 8X There is a 5.41% of reference with a coverageData >= 9X There is a 4.96% of reference with a coverageData >= 10X There is a 4.63% of reference with a coverageData >= 11X There is a 4.37% of reference with a coverageData >= 12X There is a 4.16% of reference with a coverageData >= 13X There is a 3.98% of reference with a coverageData >= 14X There is a 3.83% of reference with a coverageData >= 15X There is a 3.69% of reference with a coverageData >= 16X There is a 3.57% of reference with a coverageData >= 17X There is a 3.46% of reference with a coverageData >= 18X There is a 3.36% of reference with a coverageData >= 19X There is a 3.26% of reference with a coverageData >= 20X There is a 3.17% of reference with a coverageData >= 21X There is a 3.09% of reference with a coverageData >= 22X There is a 3.01% of reference with a coverageData >= 23X There is a 2.94% of reference with a coverageData >= 24X There is a 2.87% of reference with a coverageData >= 25X There is a 2.8% of reference with a coverageData >= 26X There is a 2.73% of reference with a coverageData >= 27X There is a 2.67% of reference with a coverageData >= 28X There is a 2.61% of reference with a coverageData >= 29X There is a 2.56% of reference with a coverageData >= 30X There is a 2.5% of reference with a coverageData >= 31X There is a 2.45% of reference with a coverageData >= 32X There is a 2.4% of reference with a coverageData >= 33X There is a 2.35% of reference with a coverageData >= 34X There is a 2.31% of reference with a coverageData >= 35X There is a 2.26% of reference with a coverageData >= 36X There is a 2.22% of reference with a coverageData >= 37X There is a 2.18% of reference with a coverageData >= 38X There is a 2.14% of reference with a coverageData >= 39X There is a 2.1% of reference with a coverageData >= 40X There is a 2.06% of reference with a coverageData >= 41X There is a 2.02% of reference with a coverageData >= 42X There is a 1.99% of reference with a coverageData >= 43X There is a 1.95% of reference with a coverageData >= 44X There is a 1.92% of reference with a coverageData >= 45X There is a 1.88% of reference with a coverageData >= 46X There is a 1.85% of reference with a coverageData >= 47X There is a 1.82% of reference with a coverageData >= 48X There is a 1.79% of reference with a coverageData >= 49X There is a 1.76% of reference with a coverageData >= 50X There is a 1.73% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1373712421 5.5113701040688685 40.36595277094773 chr2 243199373 950227319 3.9071947730720504 22.586477441884192 chr3 198022430 825087914 4.166638668154915 23.886000381219596 chr4 191154276 649911278 3.399930629854181 29.956513000250517 chr5 180915260 1007876433 5.570986289382112 63.013499619283714 chr6 171115067 407899693 2.383774264600557 16.140284150242756 chr7 159138663 886731983 5.572071338817268 43.51772715007756 chr8 146364022 1008930320 6.893294583008931 91.32374535257817 chr9 141213431 466617786 3.3043442305427733 22.494792790132472 chr10 135534747 725650009 5.35397767039031 32.65852469139088 chr11 135006516 744257804 5.512754688077425 28.23609791988923 chr12 133851895 584162789 4.364247431835015 23.241272513249843 chr13 115169878 180063655 1.5634613679108005 11.809951101497097 chr14 107349540 417040741 3.8848861485573205 23.590716913405103 chr15 102531392 655257499 6.390798819936045 37.44948193597304 chr16 90354753 596347413 6.600066883033812 43.313809304331826 chr17 81195210 440039376 5.419523836443061 30.784568397475972 chr18 78077248 147158468 1.8847804164409074 13.042389302678526 chr19 59128983 696991211 11.787640775083178 53.08904490602209 chr20 63025520 266026649 4.220935408386952 22.696041446606717 chr21 48129895 142890245 2.9688459740043065 32.05778104318839 chr22 51304566 159380505 3.106555954493407 21.10076267237944 chrMT 16571 27866 1.6816124554945386 1.6562489449229711 chrX 155270560 1049467889 6.758962478141381 39.863260829639344 chrY 59373566 17525831 0.2951790195657104 11.000189429196459