BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094126.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 474,174 number of mapped reads = 444,762 (93.8%) number of supplementary alignments = 832 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 223,055 number of mapped paired reads (second in pair) = 221,707 number of mapped paired reads (both in pair) = 442,782 number of mapped paired reads (singletons) = 1,980 number of mapped bases = 65,608,067 bp number of sequenced bases = 65,555,762 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 442,229 duplication rate = 50.73% >>>>>>> Insert size mean insert size = 4,467.92 std insert size = 572,725.8164 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 20.0497 >>>>>>> ACTG content number of A's = 18,049,084 bp (27.53%) number of C's = 14,009,297 bp (21.37%) number of T's = 18,833,254 bp (28.73%) number of G's = 14,663,393 bp (22.37%) number of N's = 734 bp (0%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 1,043,993 number of insertions = 18,591 mapped reads with insertion percentage = 4.14% number of deletions = 44,885 mapped reads with deletion percentage = 9.89% homopolymer indels = 64.9% >>>>>>> Coverage mean coverageData = 0.0212X std coverageData = 36.8209X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 57736 2.3163833962925212E-4 0.15492862987946251 chr2 243199373 191023 7.854584394837236E-4 0.7318031497317172 chr3 198022430 12480 6.302316358808444E-5 0.04428028520927188 chr4 191154276 11334 5.929242200158787E-5 0.0162835525285833 chr5 180915260 11460 6.334457358655096E-5 0.017727825062649614 chr6 171115067 4662 2.7244824676952614E-5 0.007988124830040732 chr7 159138663 6485 4.075062513249844E-5 0.011357784981382464 chr8 146364022 6637 4.5345843256480065E-5 0.020214086734872082 chr9 141213431 5825 4.1249617396520875E-5 0.014704086253414114 chr10 135534747 1244913 0.009185194406272806 3.992587277092033 chr11 135006516 7300 5.407146422473416E-5 0.02282675907135567 chr12 133851895 6650 4.96817770118234E-5 0.014222288139155595 chr13 115169878 15137 1.3143193570110408E-4 0.09381216100943492 chr14 107349540 7035 6.553358309686282E-5 0.05805399519064877 chr15 102531392 3580 3.491613573333716E-5 0.009034525867106975 chr16 90354753 7635 8.45002586637584E-5 0.06489311315440541 chr17 81195210 3699 4.5556874598883356E-5 0.011092106150520996 chr18 78077248 1030 1.3192063326822175E-5 0.005183691432129938 chr19 59128983 1292 2.185053647887027E-5 0.007219616513270325 chr20 63025520 1716 2.7227066115440222E-5 0.00782384766216264 chr21 48129895 804 1.6704794390264098E-5 0.006794590338641079 chr22 51304566 698 1.3605026889809379E-5 0.007400727704055421 chrMT 16571 63880690 3854.9689216100414 15437.019454549469 chrX 155270560 114456 7.371390944941527E-4 0.06918280448451823 chrY 59373566 3790 6.383312061802048E-5 0.023054910220006247