BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124985.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,932,142 number of mapped reads = 4,699,101 (95.28%) number of supplementary alignments = 17,224 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,396,517 number of mapped paired reads (second in pair) = 2,302,584 number of mapped paired reads (both in pair) = 4,573,870 number of mapped paired reads (singletons) = 125,231 number of mapped bases = 286,290,301 bp number of sequenced bases = 286,136,517 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 372,243 duplication rate = 4.42% >>>>>>> Insert size mean insert size = 78,767.7364 std insert size = 2,649,353.31 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 51.4952 >>>>>>> ACTG content number of A's = 79,440,119 bp (27.76%) number of C's = 50,256,634 bp (17.56%) number of T's = 86,632,824 bp (30.28%) number of G's = 69,806,939 bp (24.4%) number of N's = 1 bp (0%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 2,233,613 number of insertions = 39,684 mapped reads with insertion percentage = 0.83% number of deletions = 93,627 mapped reads with deletion percentage = 1.97% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.0925X std coverageData = 1.3144X There is a 7.13% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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% 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 24225390 0.0971928972646371 0.566169842064587 chr2 243199373 23231277 0.09552358919938499 1.3875989280287124 chr3 198022430 19973691 0.10086580090952323 0.46010881426603356 chr4 191154276 18828026 0.09849649400466459 1.3506007580162964 chr5 180915260 17071646 0.09436266459777909 0.3789134761567343 chr6 171115067 16771413 0.09801248536459972 0.4600902218287055 chr7 159138663 15962955 0.10030846495172578 0.6156714006853052 chr8 146364022 16441612 0.11233369905617925 0.445575948669731 chr9 141213431 11694883 0.08281707283211609 0.6925056014819033 chr10 135534747 18330424 0.13524520025849904 4.8497652373811455 chr11 135006516 13274790 0.09832703185970668 0.4691366701387602 chr12 133851895 12102684 0.09041847334324254 0.3622162467876328 chr13 115169878 7473600 0.06489196767231098 0.29552125556041875 chr14 107349540 7254975 0.06758273021011547 0.3741037900525307 chr15 102531392 6981428 0.06809063901131861 0.3133500511093612 chr16 90354753 10558619 0.11685737218494748 2.028805591080895 chr17 81195210 6852293 0.08439282317269702 0.560237761066436 chr18 78077248 7297673 0.09346734403343725 0.9666141257979103 chr19 59128983 4349724 0.07356331496518383 0.5437257900662752 chr20 63025520 5077441 0.0805616677180926 0.5610666788588096 chr21 48129895 3798568 0.07892325549432426 0.6862649493918163 chr22 51304566 3066324 0.05976707804135795 0.3425327710467812 chrMT 16571 130160 7.854685897049062 5.367578985395742 chrX 155270560 9301575 0.0599055931787713 0.35959099187845917 chrY 59373566 6239130 0.10508262212177048 2.467530475505551