BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961017.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 305,517,976 number of mapped reads = 298,421,867 (97.68%) number of supplementary alignments = 682,493 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 149,383,319 number of mapped paired reads (second in pair) = 149,038,548 number of mapped paired reads (both in pair) = 297,427,442 number of mapped paired reads (singletons) = 994,425 number of mapped bases = 29,309,573,800 bp number of sequenced bases = 29,300,506,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,032,266 duplication rate = 8.34% >>>>>>> Insert size mean insert size = 21,774.3899 std insert size = 1,374,091.6575 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.6594 >>>>>>> ACTG content number of A's = 8,632,148,906 bp (29.46%) number of C's = 5,994,375,814 bp (20.46%) number of T's = 8,610,013,289 bp (29.39%) number of G's = 6,044,847,037 bp (20.63%) number of N's = 19,121,401 bp (0.07%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 144,203,771 number of insertions = 3,016,668 mapped reads with insertion percentage = 0.97% number of deletions = 3,578,264 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.64% >>>>>>> Coverage mean coverageData = 9.4679X std coverageData = 104.1264X There is a 91.43% of reference with a coverageData >= 1X There is a 90.84% of reference with a coverageData >= 2X There is a 89.56% of reference with a coverageData >= 3X There is a 87.21% of reference with a coverageData >= 4X There is a 83.42% of reference with a coverageData >= 5X There is a 78.06% of reference with a coverageData >= 6X There is a 71.16% of reference with a coverageData >= 7X There is a 63.08% of reference with a coverageData >= 8X There is a 54.29% of reference with a coverageData >= 9X There is a 45.34% of reference with a coverageData >= 10X There is a 36.76% of reference with a coverageData >= 11X There is a 28.96% of reference with a coverageData >= 12X There is a 22.2% of reference with a coverageData >= 13X There is a 16.59% of reference with a coverageData >= 14X There is a 12.11% of reference with a coverageData >= 15X There is a 8.67% of reference with a coverageData >= 16X There is a 6.1% of reference with a coverageData >= 17X There is a 4.24% of reference with a coverageData >= 18X There is a 2.93% of reference with a coverageData >= 19X There is a 2.02% of reference with a coverageData >= 20X There is a 1.41% of reference with a coverageData >= 21X There is a 1.01% of reference with a coverageData >= 22X There is a 0.74% of reference with a coverageData >= 23X There is a 0.57% of reference with a coverageData >= 24X There is a 0.45% of reference with a coverageData >= 25X There is a 0.38% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.29% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2384627503 9.56718781053709 247.70175268320895 chr2 243199373 2511148130 10.325471233842366 64.91976542263973 chr3 198022430 1927544646 9.733971277900185 21.29679149164358 chr4 191154276 1972572776 10.319270995538703 91.39348918748937 chr5 180915260 1758371334 9.71930910637389 10.127782646688662 chr6 171115067 1676113314 9.795240964958392 30.27944837994629 chr7 159138663 1563878077 9.827140982075488 63.51686795327646 chr8 146364022 1471955507 10.056812370187531 102.11465838040583 chr9 141213431 1222769076 8.659013999879374 88.97238782022157 chr10 135534747 1533940150 11.317689256467938 245.41599212761017 chr11 135006516 1319828905 9.776038550613364 41.11613639340535 chr12 133851895 1291187981 9.646392985321574 7.93672760623734 chr13 115169878 930754152 8.08157626076499 5.868703606170801 chr14 107349540 863028432 8.039423662178711 9.207664243884393 chr15 102531392 812287548 7.922330245940677 5.990345496254036 chr16 90354753 941748076 10.422784023326365 100.57922359451 chr17 81195210 784509973 9.662022833612967 38.56187202493641 chr18 78077248 797359494 10.212443630185327 106.14270337767016 chr19 59128983 571691295 9.668546049574369 119.63827701247274 chr20 63025520 604143817 9.585701426977517 34.13638394686601 chr21 48129895 402280721 8.358229765512682 45.22552199724308 chr22 51304566 344466809 6.714155013025547 8.046310007289554 chrMT 16571 22474936 1356.2812141693319 194.04779842478445 chrX 155270560 1502355876 9.67572910151158 31.41766208781055 chrY 59373566 98535272 1.6595815046716245 96.77425454541836