BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046428.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 8,389,388 number of mapped reads = 8,350,386 (99.54%) number of supplementary alignments = 49,977 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,178,802 number of mapped paired reads (second in pair) = 4,171,584 number of mapped paired reads (both in pair) = 8,323,334 number of mapped paired reads (singletons) = 27,052 number of mapped bases = 810,893,806 bp number of sequenced bases = 810,644,550 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,405,848 duplication rate = 39.73% >>>>>>> Insert size mean insert size = 17,712.1563 std insert size = 1,320,658.0383 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 51.5957 >>>>>>> ACTG content number of A's = 241,120,298 bp (29.74%) number of C's = 164,068,833 bp (20.24%) number of T's = 242,255,832 bp (29.88%) number of G's = 163,126,586 bp (20.12%) number of N's = 73,001 bp (0.01%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 3,180,788 number of insertions = 70,897 mapped reads with insertion percentage = 0.83% number of deletions = 94,576 mapped reads with deletion percentage = 1.1% homopolymer indels = 49.31% >>>>>>> Coverage mean coverageData = 0.2619X std coverageData = 25.5671X There is a 2.3% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 163861866 0.6574180852291638 43.68043502968194 chr2 243199373 126170219 0.5187933564285957 37.207039258608205 chr3 198022430 4004890 0.020224426091529125 1.543540441628876 chr4 191154276 18164899 0.09502742695643387 5.1581818552506595 chr5 180915260 51598955 0.28521062844560485 24.000637360405516 chr6 171115067 14494710 0.08470738582009263 9.53707080175721 chr7 159138663 92198368 0.5793586942476701 39.15409848298937 chr8 146364022 86715673 0.5924657700373934 41.80155690964571 chr9 141213431 17155323 0.12148506610536218 19.146995867312285 chr10 135534747 17975234 0.13262454387434686 13.560830700365498 chr11 135006516 14201478 0.10519105611169167 3.7459268301994144 chr12 133851895 20177982 0.15074857177031376 9.721794020642742 chr13 115169878 9210998 0.07997749203137994 5.624086308998367 chr14 107349540 39983607 0.3724618382156086 25.68029851997401 chr15 102531392 14013341 0.13667366380825105 9.036362645936638 chr16 90354753 32250221 0.35692888231347386 34.62371215978734 chr17 81195210 9298044 0.11451468627274934 7.78834533054449 chr18 78077248 1625482 0.020818894641368508 0.8811898775437522 chr19 59128983 7440165 0.12582940924250297 6.008060173057869 chr20 63025520 4065459 0.06450496560758245 7.175947821974828 chr21 48129895 6544851 0.13598307247501787 17.87975958288181 chr22 51304566 7677973 0.1496547695189547 9.067183080941767 chrMT 16571 27178 1.640094140365699 1.716244516719462 chrX 155270560 51854806 0.333964184839676 41.993138883170694 chrY 59373566 182084 0.0030667519616389555 0.2893549738831679