BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104292.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 522,209,866 number of mapped reads = 484,020,173 (92.69%) number of supplementary alignments = 300,156 (0.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 249,842,017 number of mapped paired reads (second in pair) = 234,178,156 number of mapped paired reads (both in pair) = 467,448,922 number of mapped paired reads (singletons) = 16,571,251 number of mapped bases = 30,389,811,790 bp number of sequenced bases = 30,384,627,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 305,697,815 duplication rate = 39.5% >>>>>>> Insert size mean insert size = 21,231.1591 std insert size = 1,292,068.037 median insert size = 57 >>>>>>> Mapping quality mean mapping quality = 50.4443 >>>>>>> ACTG content number of A's = 8,422,037,473 bp (27.72%) number of C's = 7,020,133,233 bp (23.1%) number of T's = 8,542,607,696 bp (28.11%) number of G's = 6,393,275,200 bp (21.04%) number of N's = 6,573,482 bp (0.02%) GC percentage = 44.15% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 152,858,957 number of insertions = 2,219,067 mapped reads with insertion percentage = 0.45% number of deletions = 2,460,790 mapped reads with deletion percentage = 0.5% homopolymer indels = 40.16% >>>>>>> Coverage mean coverageData = 9.8168X std coverageData = 172.3024X There is a 87.67% of reference with a coverageData >= 1X There is a 82.22% of reference with a coverageData >= 2X There is a 74.8% of reference with a coverageData >= 3X There is a 67.33% of reference with a coverageData >= 4X There is a 59.52% of reference with a coverageData >= 5X There is a 52.43% of reference with a coverageData >= 6X There is a 45.72% of reference with a coverageData >= 7X There is a 39.9% of reference with a coverageData >= 8X There is a 34.65% of reference with a coverageData >= 9X There is a 30.2% of reference with a coverageData >= 10X There is a 26.28% of reference with a coverageData >= 11X There is a 22.98% of reference with a coverageData >= 12X There is a 20.11% of reference with a coverageData >= 13X There is a 17.7% of reference with a coverageData >= 14X There is a 15.61% of reference with a coverageData >= 15X There is a 13.86% of reference with a coverageData >= 16X There is a 12.34% of reference with a coverageData >= 17X There is a 11.05% of reference with a coverageData >= 18X There is a 9.94% of reference with a coverageData >= 19X There is a 8.99% of reference with a coverageData >= 20X There is a 8.16% of reference with a coverageData >= 21X There is a 7.45% of reference with a coverageData >= 22X There is a 6.82% of reference with a coverageData >= 23X There is a 6.28% of reference with a coverageData >= 24X There is a 5.8% of reference with a coverageData >= 25X There is a 5.39% of reference with a coverageData >= 26X There is a 5.01% of reference with a coverageData >= 27X There is a 4.69% of reference with a coverageData >= 28X There is a 4.39% of reference with a coverageData >= 29X There is a 4.13% of reference with a coverageData >= 30X There is a 3.9% of reference with a coverageData >= 31X There is a 3.69% of reference with a coverageData >= 32X There is a 3.49% of reference with a coverageData >= 33X There is a 3.32% of reference with a coverageData >= 34X There is a 3.16% of reference with a coverageData >= 35X There is a 3.01% of reference with a coverageData >= 36X There is a 2.88% of reference with a coverageData >= 37X There is a 2.76% of reference with a coverageData >= 38X There is a 2.64% of reference with a coverageData >= 39X There is a 2.54% of reference with a coverageData >= 40X There is a 2.44% of reference with a coverageData >= 41X There is a 2.35% of reference with a coverageData >= 42X There is a 2.26% of reference with a coverageData >= 43X There is a 2.18% of reference with a coverageData >= 44X There is a 2.11% of reference with a coverageData >= 45X There is a 2.03% of reference with a coverageData >= 46X There is a 1.97% of reference with a coverageData >= 47X There is a 1.9% of reference with a coverageData >= 48X There is a 1.84% of reference with a coverageData >= 49X There is a 1.79% of reference with a coverageData >= 50X There is a 1.73% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2404845330 9.64830226039838 251.25198355767364 chr2 243199373 2568364153 10.560735092849109 59.834877249566496 chr3 198022430 2029308246 10.247870637684832 31.08465027455097 chr4 191154276 2160457049 11.30216437847302 39.286610487322015 chr5 180915260 1924691949 10.638637940215768 45.67554977044003 chr6 171115067 1789475372 10.45773118272513 38.06504666229392 chr7 159138663 1648796322 10.360752634952073 92.32486062369597 chr8 146364022 1532645205 10.471461388236516 51.66179070717281 chr9 141213431 1269830689 8.992279841993216 51.56062952793987 chr10 135534747 1421833586 10.490546649266259 161.1275177607484 chr11 135006516 1338424532 9.913777287608845 60.56851641092376 chr12 133851895 1277385245 9.54327351883961 25.350511624870233 chr13 115169878 986183877 8.562862912818229 35.83732201872169 chr14 107349540 867207112 8.07834958584825 25.408153319166132 chr15 102531392 697453665 6.802342691299851 14.39877723292229 chr16 90354753 816295271 9.034336810150984 63.55985632318709 chr17 81195210 668193336 8.229467427943101 34.63508319562233 chr18 78077248 795780791 10.192223872952079 87.25601021661798 chr19 59128983 533699432 9.026020826368686 151.33280024429314 chr20 63025520 521167875 8.269156287802147 19.73786714142682 chr21 48129895 385909275 8.018078472849359 34.677580441289514 chr22 51304566 276785540 5.394949447579383 68.6064969091695 chrMT 16571 905058602 54617.01780218454 30327.9516021289 chrX 155270560 1473460197 9.4896302106465 27.75313578533764 chrY 59373566 96559139 1.6262984608335636 59.587177070523396