BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472574.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 = 10,975,908 number of mapped reads = 10,053,677 (91.6%) number of supplementary alignments = 289,126 (2.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,071,785 number of mapped paired reads (second in pair) = 4,981,892 number of mapped paired reads (both in pair) = 9,806,618 number of mapped paired reads (singletons) = 247,059 number of mapped bases = 811,950,138 bp number of sequenced bases = 811,589,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,701,166 duplication rate = 14.51% >>>>>>> Insert size mean insert size = 220,066.1942 std insert size = 4,561,607.1979 median insert size = 126 >>>>>>> Mapping quality mean mapping quality = 50.1702 >>>>>>> ACTG content number of A's = 207,358,707 bp (25.55%) number of C's = 163,833,634 bp (20.19%) number of T's = 239,941,267 bp (29.56%) number of G's = 199,915,792 bp (24.63%) number of N's = 540,085 bp (0.07%) GC percentage = 44.82% >>>>>>> Mismatches and indels general error rate = 0.0125 number of mismatches = 9,951,745 number of insertions = 82,144 mapped reads with insertion percentage = 0.8% number of deletions = 189,607 mapped reads with deletion percentage = 1.85% homopolymer indels = 42.44% >>>>>>> Coverage mean coverageData = 0.2623X std coverageData = 2.5141X There is a 13.74% of reference with a coverageData >= 1X There is a 6.53% of reference with a coverageData >= 2X There is a 2.48% of reference with a coverageData >= 3X There is a 1.24% of reference with a coverageData >= 4X There is a 0.6% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% 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 53178768 0.21335460584469315 3.4205110112341277 chr2 243199373 80448267 0.3307914243676936 3.5896579495263383 chr3 198022430 42107407 0.2126395833037702 0.713063954002208 chr4 191154276 40269864 0.21066682285464544 1.4464633145043748 chr5 180915260 37600829 0.20783669105635422 0.7566154912208858 chr6 171115067 53645720 0.31350670014347715 1.4149432691251929 chr7 159138663 68761310 0.4320842509528938 4.841972951333314 chr8 146364022 39246813 0.2681452208248281 2.2057709135779446 chr9 141213431 28285951 0.2003063787891394 2.8221108925676477 chr10 135534747 31742327 0.23420065852190655 2.4587033505831166 chr11 135006516 29520346 0.21865867570421563 1.8332211114524195 chr12 133851895 41330820 0.3087802380384678 0.9131098046392414 chr13 115169878 37363542 0.32442113032367714 0.9399455288074196 chr14 107349540 20490229 0.1908739338799216 4.673851478615614 chr15 102531392 19181816 0.18708237180667556 0.6830677017566923 chr16 90354753 30434856 0.33683735486499533 1.5392693934366017 chr17 81195210 32610495 0.4016307735394736 2.0648342922469007 chr18 78077248 17721804 0.22697782585779663 4.633122678131607 chr19 59128983 19029850 0.32183624737804134 2.4204626560488194 chr20 63025520 28609656 0.4539376430372966 1.4286593965803072 chr21 48129895 12146264 0.25236423225107807 1.0715404400347313 chr22 51304566 9828242 0.19156661416841533 0.7084747793161279 chrMT 16571 263784 15.91841168306077 10.520482276038381 chrX 155270560 36134667 0.23272065870052894 1.1596898648244793 chrY 59373566 1996511 0.03362626054833897 1.2773664536750844