BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926988.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 20,386,082 number of mapped reads = 20,003,908 (98.13%) number of supplementary alignments = 483,987 (2.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,042,967 number of mapped paired reads (second in pair) = 9,960,941 number of mapped paired reads (both in pair) = 19,781,132 number of mapped paired reads (singletons) = 222,776 number of mapped bases = 1,862,657,358 bp number of sequenced bases = 1,861,249,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,376,787 duplication rate = 5.41% >>>>>>> Insert size mean insert size = 254,067.2804 std insert size = 4,957,222.5135 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 52.7083 >>>>>>> ACTG content number of A's = 532,995,967 bp (28.64%) number of C's = 368,853,294 bp (19.82%) number of T's = 542,098,847 bp (29.13%) number of G's = 417,151,860 bp (22.41%) number of N's = 149,919 bp (0.01%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 17,588,036 number of insertions = 320,395 mapped reads with insertion percentage = 1.57% number of deletions = 966,241 mapped reads with deletion percentage = 4.71% homopolymer indels = 52.13% >>>>>>> Coverage mean coverageData = 0.6017X std coverageData = 2.4111X There is a 28.39% of reference with a coverageData >= 1X There is a 14.2% of reference with a coverageData >= 2X There is a 7.11% of reference with a coverageData >= 3X There is a 3.89% of reference with a coverageData >= 4X There is a 2.19% of reference with a coverageData >= 5X There is a 1.28% of reference with a coverageData >= 6X There is a 0.77% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 148919106 0.5974673419168733 2.8737295691126805 chr2 243199373 166688196 0.6853973098030972 4.073513640601244 chr3 198022430 130177845 0.6573893927066747 1.367021969162785 chr4 191154276 111284071 0.5821688812234574 1.9677298873627083 chr5 180915260 112757796 0.6232630459144243 1.3188511899455124 chr6 171115067 109013703 0.6370783409739131 1.6934854684909284 chr7 159138663 99979749 0.6282555547170834 1.9762003078179557 chr8 146364022 96824897 0.6615348203535976 1.6259531967468284 chr9 141213431 80043046 0.5668231798716087 3.0209717090843986 chr10 135534747 91652281 0.6762271891797607 3.4497345528881977 chr11 135006516 90520128 0.67048710448909 3.183970138427274 chr12 133851895 84011394 0.6276444125053291 1.6343313199740928 chr13 115169878 53830883 0.4674041853200539 1.2173881900598087 chr14 107349540 54876146 0.5111912542894921 1.2427375499938493 chr15 102531392 50294523 0.49052804237749936 1.2594460466796003 chr16 90354753 55970168 0.619449073143944 4.161680141575073 chr17 81195210 45306737 0.5579976577436033 1.6983199560339761 chr18 78077248 50701561 0.6493768965832403 3.145926769010614 chr19 59128983 27655107 0.46770814576668773 1.8851909407994891 chr20 63025520 43031747 0.6827670283402659 1.4962158724576957 chr21 48129895 22827946 0.4742986869179748 1.7729893611398924 chr22 51304566 22403265 0.43667195235605344 1.1938605829814601 chrMT 16571 193282 11.663870617343552 10.702001472457276 chrX 155270560 110421545 0.7111557078173738 1.7649138350048064 chrY 59373566 3272236 0.05511267421599707 1.756853692587395