BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16362017.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 1,565,782,248 number of mapped reads = 1,541,168,499 (98.43%) number of supplementary alignments = 67,511,084 (4.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 773,089,795 number of mapped paired reads (second in pair) = 768,078,704 number of mapped paired reads (both in pair) = 1,530,316,416 number of mapped paired reads (singletons) = 10,852,083 number of mapped bases = 215,548,653,538 bp number of sequenced bases = 215,369,209,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 698,145,813 duplication rate = 40.82% >>>>>>> Insert size mean insert size = 170,702.8856 std insert size = 4,047,151.6218 median insert size = 279 >>>>>>> Mapping quality mean mapping quality = 53.8322 >>>>>>> ACTG content number of A's = 62,001,820,167 bp (28.79%) number of C's = 45,257,288,082 bp (21.01%) number of T's = 61,403,282,921 bp (28.51%) number of G's = 46,702,787,600 bp (21.68%) number of N's = 4,031,065 bp (0%) GC percentage = 42.7% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,670,588,867 number of insertions = 37,841,345 mapped reads with insertion percentage = 2.34% number of deletions = 98,859,424 mapped reads with deletion percentage = 6.16% homopolymer indels = 44.99% >>>>>>> Coverage mean coverageData = 69.6285X std coverageData = 945.7837X There is a 91.71% of reference with a coverageData >= 1X There is a 91.62% of reference with a coverageData >= 2X There is a 91.56% of reference with a coverageData >= 3X There is a 91.52% of reference with a coverageData >= 4X There is a 91.48% of reference with a coverageData >= 5X There is a 91.45% of reference with a coverageData >= 6X There is a 91.43% of reference with a coverageData >= 7X There is a 91.4% of reference with a coverageData >= 8X There is a 91.38% of reference with a coverageData >= 9X There is a 91.35% of reference with a coverageData >= 10X There is a 91.33% of reference with a coverageData >= 11X There is a 91.31% of reference with a coverageData >= 12X There is a 91.28% of reference with a coverageData >= 13X There is a 91.26% of reference with a coverageData >= 14X There is a 91.23% of reference with a coverageData >= 15X There is a 91.21% of reference with a coverageData >= 16X There is a 91.18% of reference with a coverageData >= 17X There is a 91.16% of reference with a coverageData >= 18X There is a 91.13% of reference with a coverageData >= 19X There is a 91.1% of reference with a coverageData >= 20X There is a 91.06% of reference with a coverageData >= 21X There is a 91.03% of reference with a coverageData >= 22X There is a 90.99% of reference with a coverageData >= 23X There is a 90.95% of reference with a coverageData >= 24X There is a 90.91% of reference with a coverageData >= 25X There is a 90.86% of reference with a coverageData >= 26X There is a 90.81% of reference with a coverageData >= 27X There is a 90.75% of reference with a coverageData >= 28X There is a 90.68% of reference with a coverageData >= 29X There is a 90.6% of reference with a coverageData >= 30X There is a 90.52% of reference with a coverageData >= 31X There is a 90.42% of reference with a coverageData >= 32X There is a 90.3% of reference with a coverageData >= 33X There is a 90.17% of reference with a coverageData >= 34X There is a 90.01% of reference with a coverageData >= 35X There is a 89.84% of reference with a coverageData >= 36X There is a 89.63% of reference with a coverageData >= 37X There is a 89.39% of reference with a coverageData >= 38X There is a 89.12% of reference with a coverageData >= 39X There is a 88.81% of reference with a coverageData >= 40X There is a 88.45% of reference with a coverageData >= 41X There is a 88.04% of reference with a coverageData >= 42X There is a 87.58% of reference with a coverageData >= 43X There is a 87.06% of reference with a coverageData >= 44X There is a 86.48% of reference with a coverageData >= 45X There is a 85.83% of reference with a coverageData >= 46X There is a 85.11% of reference with a coverageData >= 47X There is a 84.31% of reference with a coverageData >= 48X There is a 83.43% of reference with a coverageData >= 49X There is a 82.48% of reference with a coverageData >= 50X There is a 81.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17675768841 70.9156461479789 1482.6554509043283 chr2 243199373 18629354995 76.60116374971082 2517.5487087390707 chr3 198022430 14022462001 70.81249331704494 54.74186771963567 chr4 191154276 13754497462 71.95495570290042 603.9984636881792 chr5 180915260 12764445983 70.55483314674505 46.57892184836741 chr6 171115067 12076545514 70.57558241788259 153.1659324258661 chr7 159138663 11604981858 72.92371092749472 456.63795700960105 chr8 146364022 10502816180 71.75818234893818 793.8217102107393 chr9 141213431 9244005300 65.46123293328947 764.7590164554363 chr10 135534747 10824962554 79.86854141543496 1130.0028463789508 chr11 135006516 9711378213 71.93266296124551 300.3887927722928 chr12 133851895 9565860889 71.46601016743169 99.05658189301094 chr13 115169878 6610339106 57.39642362041922 36.47258288627588 chr14 107349540 6442024629 60.00980189575102 65.3835201201207 chr15 102531392 6046593432 58.97309413296564 41.48501551915883 chr16 90354753 7107080039 78.65751167511907 615.9388954426279 chr17 81195210 6255874077 77.04732923284514 374.4782936189096 chr18 78077248 5769132948 73.8900652338566 744.986811682553 chr19 59128983 4576062438 77.391191355346 887.0734996529244 chr20 63025520 4525754075 71.80827821809324 178.42462070075257 chr21 48129895 2902822975 60.31226486157927 276.1646867302912 chr22 51304566 2715716446 52.93323105003948 58.11779089539792 chrMT 16571 782016983 47191.900488805746 6650.026856816506 chrX 155270560 10789382388 69.48762462117739 147.54767368037514 chrY 59373566 648774212 10.926987474526964 676.0337978642189