BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618621.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 40,893,424 number of mapped reads = 37,426,212 (91.52%) number of supplementary alignments = 96,682 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 19,062,780 number of mapped paired reads (second in pair) = 18,363,432 number of mapped paired reads (both in pair) = 35,868,388 number of mapped paired reads (singletons) = 1,557,824 number of mapped bases = 3,506,892,369 bp number of sequenced bases = 3,504,730,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,759,794 duplication rate = 42.8% >>>>>>> Insert size mean insert size = 76,513.32 std insert size = 2,840,106.3903 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.7269 >>>>>>> ACTG content number of A's = 870,166,972 bp (24.83%) number of C's = 860,543,507 bp (24.55%) number of T's = 880,825,624 bp (25.13%) number of G's = 890,327,163 bp (25.4%) number of N's = 2,867,145 bp (0.08%) GC percentage = 49.96% >>>>>>> Mismatches and indels general error rate = 0.0151 number of mismatches = 52,038,531 number of insertions = 646,001 mapped reads with insertion percentage = 1.7% number of deletions = 1,553,041 mapped reads with deletion percentage = 4.06% homopolymer indels = 51.65% >>>>>>> Coverage mean coverageData = 1.1328X std coverageData = 6.7044X There is a 14.01% of reference with a coverageData >= 1X There is a 10.09% of reference with a coverageData >= 2X There is a 7.99% of reference with a coverageData >= 3X There is a 6.71% of reference with a coverageData >= 4X There is a 5.74% of reference with a coverageData >= 5X There is a 5.02% of reference with a coverageData >= 6X There is a 4.43% of reference with a coverageData >= 7X There is a 3.96% of reference with a coverageData >= 8X There is a 3.56% of reference with a coverageData >= 9X There is a 3.22% of reference with a coverageData >= 10X There is a 2.93% of reference with a coverageData >= 11X There is a 2.67% of reference with a coverageData >= 12X There is a 2.45% of reference with a coverageData >= 13X There is a 2.25% of reference with a coverageData >= 14X There is a 2.07% of reference with a coverageData >= 15X There is a 1.92% of reference with a coverageData >= 16X There is a 1.78% of reference with a coverageData >= 17X There is a 1.65% of reference with a coverageData >= 18X There is a 1.53% of reference with a coverageData >= 19X There is a 1.43% of reference with a coverageData >= 20X There is a 1.33% of reference with a coverageData >= 21X There is a 1.25% of reference with a coverageData >= 22X There is a 1.17% of reference with a coverageData >= 23X There is a 1.09% of reference with a coverageData >= 24X There is a 1.03% of reference with a coverageData >= 25X There is a 0.96% of reference with a coverageData >= 26X There is a 0.9% of reference with a coverageData >= 27X There is a 0.85% of reference with a coverageData >= 28X There is a 0.8% of reference with a coverageData >= 29X There is a 0.76% of reference with a coverageData >= 30X There is a 0.71% of reference with a coverageData >= 31X There is a 0.68% of reference with a coverageData >= 32X There is a 0.64% of reference with a coverageData >= 33X There is a 0.61% of reference with a coverageData >= 34X There is a 0.58% of reference with a coverageData >= 35X There is a 0.55% of reference with a coverageData >= 36X There is a 0.52% of reference with a coverageData >= 37X There is a 0.49% of reference with a coverageData >= 38X There is a 0.47% of reference with a coverageData >= 39X There is a 0.45% of reference with a coverageData >= 40X There is a 0.43% of reference with a coverageData >= 41X There is a 0.41% of reference with a coverageData >= 42X There is a 0.39% of reference with a coverageData >= 43X There is a 0.37% of reference with a coverageData >= 44X There is a 0.35% of reference with a coverageData >= 45X There is a 0.34% of reference with a coverageData >= 46X There is a 0.32% of reference with a coverageData >= 47X There is a 0.31% of reference with a coverageData >= 48X There is a 0.29% of reference with a coverageData >= 49X There is a 0.28% of reference with a coverageData >= 50X There is a 0.27% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 347576635 1.3944865357025529 7.5180288496848195 chr2 243199373 286265545 1.1770817558810072 7.1166538824667676 chr3 198022430 207419503 1.047454588856424 5.552568464565078 chr4 191154276 146267685 0.7651813397048989 5.283158362065189 chr5 180915260 184107949 1.017647427862083 5.299791007723771 chr6 171115067 175218290 1.023979320301467 5.3178070026403255 chr7 159138663 180392565 1.1335558663076113 5.964421011979764 chr8 146364022 162309517 1.1089440887324071 5.5892629240446885 chr9 141213431 159874108 1.1321451994180356 6.762237271594723 chr10 135534747 187978697 1.3869409960236987 8.951662305044579 chr11 135006516 192684156 1.4272211572365885 6.956229638752255 chr12 133851895 159791576 1.1937939018345614 6.291282225363767 chr13 115169878 79949081 0.6941839514668932 4.149651835414619 chr14 107349540 113025803 1.0528764538720892 5.995080570972914 chr15 102531392 127508234 1.2436019009670716 6.3143384024960705 chr16 90354753 152361959 1.6862639091050362 12.632257486391348 chr17 81195210 159917251 1.9695404568816313 8.375943371014039 chr18 78077248 82242862 1.0533524695952399 5.7437509358297385 chr19 59128983 115538925 1.9540150893513593 9.300827755503475 chr20 63025520 121916367 1.9343968443259174 8.093176106499852 chr21 48129895 53653315 1.1147606908346672 9.36924347736409 chr22 51304566 103242092 2.0123373034672976 9.180747613202483 chrMT 16571 9286 0.5603765614627965 2.392658609543899 chrX 155270560 4098882 0.026398320454308916 0.9295865620139744 chrY 59373566 3542086 0.059657626089024196 3.888614941481026