BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960900.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 = 98,516,884 number of mapped reads = 97,000,271 (98.46%) number of supplementary alignments = 236,637 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 48,579,712 number of mapped paired reads (second in pair) = 48,420,559 number of mapped paired reads (both in pair) = 96,597,270 number of mapped paired reads (singletons) = 403,001 number of mapped bases = 9,574,817,060 bp number of sequenced bases = 9,571,889,731 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,901,197 duplication rate = 4.1% >>>>>>> Insert size mean insert size = 23,449.7101 std insert size = 1,438,946.703 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.6343 >>>>>>> ACTG content number of A's = 2,824,481,552 bp (29.51%) number of C's = 1,956,390,807 bp (20.44%) number of T's = 2,811,633,695 bp (29.37%) number of G's = 1,979,170,691 bp (20.68%) number of N's = 212,986 bp (0%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 61,896,460 number of insertions = 1,048,484 mapped reads with insertion percentage = 1.04% number of deletions = 1,152,571 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.57% >>>>>>> Coverage mean coverageData = 3.0929X std coverageData = 33.765X There is a 82.21% of reference with a coverageData >= 1X There is a 68.97% of reference with a coverageData >= 2X There is a 51.89% of reference with a coverageData >= 3X There is a 36.36% of reference with a coverageData >= 4X There is a 23.42% of reference with a coverageData >= 5X There is a 14.24% of reference with a coverageData >= 6X There is a 8.15% of reference with a coverageData >= 7X There is a 4.49% of reference with a coverageData >= 8X There is a 2.4% of reference with a coverageData >= 9X There is a 1.28% of reference with a coverageData >= 10X There is a 0.7% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 778952147 3.125176354124309 80.84243354318023 chr2 243199373 821183789 3.376586785032542 21.32996539144328 chr3 198022430 631733476 3.190211714905226 6.731187526110357 chr4 191154276 645187666 3.3752196367294447 29.384500860829693 chr5 180915260 575841051 3.1829324458312693 3.7474868304945534 chr6 171115067 548869831 3.207606674402319 10.0275516073702 chr7 159138663 510772427 3.2096061219265115 20.806605533545994 chr8 146364022 481903698 3.2925010628636593 34.46149061347274 chr9 141213431 399496665 2.829027396126364 29.222809471667304 chr10 135534747 499275930 3.683748566705186 77.38954990131694 chr11 135006516 431124429 3.1933601560386906 13.582347630980319 chr12 133851895 422454670 3.156135144743375 4.6085051268349435 chr13 115169878 304251277 2.6417608691050276 2.5097291067658727 chr14 107349540 282421589 2.6308597968840854 3.398463913489481 chr15 102531392 265461302 2.589073422508494 2.556857861212914 chr16 90354753 304511647 3.3701785118044647 31.48822098477858 chr17 81195210 254466188 3.134004924674744 12.781627323922047 chr18 78077248 261110338 3.3442564215378083 35.155695820696884 chr19 59128983 184550109 3.121144650838997 39.53589214901948 chr20 63025520 196721883 3.121305195101921 11.442400261556925 chr21 48129895 131139683 2.7247032847256367 14.775210207288426 chr22 51304566 111286038 2.169125414685313 3.0275170852499045 chrMT 16571 7379473 445.32454287610886 66.66640969276757 chrX 155270560 492798540 3.173805388478022 10.455912857073667 chrY 59373566 31923214 0.5376671160361162 31.407811841085074