BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084853.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,560,997 number of mapped reads = 2,102,856 (82.11%) number of supplementary alignments = 19,143 (0.75%) number of secondary alignments = 0 number of mapped bases = 140,683,013 bp number of sequenced bases = 140,633,911 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,261 duplication rate = 5.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.775 >>>>>>> ACTG content number of A's = 38,369,663 bp (27.28%) number of C's = 26,655,497 bp (18.95%) number of T's = 43,914,041 bp (31.23%) number of G's = 31,673,743 bp (22.52%) number of N's = 20,967 bp (0.01%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,182,932 number of insertions = 10,219 mapped reads with insertion percentage = 0.48% number of deletions = 28,009 mapped reads with deletion percentage = 1.32% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.0454X std coverageData = 0.3097X There is a 3.67% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% 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 11241839 0.04510255162012214 0.39455998491343 chr2 243199373 11799064 0.04851601323824137 0.3490936917182774 chr3 198022430 9593152 0.04844477466517303 0.2621469261153798 chr4 191154276 9220131 0.04823397725091957 0.2688293683581952 chr5 180915260 8746787 0.048347425197852296 0.26375231159353313 chr6 171115067 8020685 0.046873049466766126 0.2740172693002953 chr7 159138663 7518733 0.04724642559049274 0.3214119884588943 chr8 146364022 6963263 0.04757496347018941 0.37443861279529667 chr9 141213431 6028759 0.042692532553790866 0.3211235023879269 chr10 135534747 6615456 0.04881003688301421 0.33195159152289094 chr11 135006516 6595681 0.048854538250583404 0.2973573296512667 chr12 133851895 6506284 0.04860808283663074 0.2678105636764763 chr13 115169878 4447394 0.03861594782621894 0.23554225550486022 chr14 107349540 4292688 0.03998794964561562 0.2500275399490628 chr15 102531392 4225244 0.04120927179063364 0.24341995430648253 chr16 90354753 3917131 0.04335279406939445 0.259315109371405 chr17 81195210 3676256 0.0452767595526879 0.2764437098278661 chr18 78077248 3985021 0.051039465427879835 0.5364263058329949 chr19 59128983 2507523 0.04240768017268283 0.3220828068271979 chr20 63025520 2986784 0.04739007310054721 0.26665377023839737 chr21 48129895 1817587 0.037764200399772324 0.2415080995313405 chr22 51304566 1582348 0.030842245113232223 0.20836269978999425 chrMT 16571 244312 14.74334681069338 7.912917969928786 chrX 155270560 7827258 0.05041044483899588 0.2848115384002331 chrY 59373566 323633 0.0054507926978817475 0.11276779174601888