BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975329.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 3,381,998 number of mapped reads = 3,326,347 (98.35%) number of supplementary alignments = 24,544 (0.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,662,173 number of mapped paired reads (second in pair) = 1,664,174 number of mapped paired reads (both in pair) = 3,308,964 number of mapped paired reads (singletons) = 17,383 number of mapped bases = 302,021,830 bp number of sequenced bases = 301,813,832 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 246,243 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 76,917.9617 std insert size = 2,645,517.065 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 52.4577 >>>>>>> ACTG content number of A's = 89,720,570 bp (29.73%) number of C's = 58,074,591 bp (19.24%) number of T's = 89,951,689 bp (29.8%) number of G's = 64,060,286 bp (21.23%) number of N's = 6,696 bp (0%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,538,877 number of insertions = 61,766 mapped reads with insertion percentage = 1.79% number of deletions = 103,796 mapped reads with deletion percentage = 3.04% homopolymer indels = 44.21% >>>>>>> Coverage mean coverageData = 0.0976X std coverageData = 1.5648X There is a 6.59% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 31881352 0.12790881672467327 1.4513844787987593 chr2 243199373 28564456 0.11745283570282888 2.063907059277094 chr3 198022430 21223350 0.10717649510714519 0.4946263049135398 chr4 191154276 15685923 0.08205897000180105 1.6580610377126295 chr5 180915260 13354135 0.07381430952811831 0.37660845076805105 chr6 171115067 18353474 0.10725808265615792 0.9212639253725374 chr7 159138663 16451847 0.1033805782319536 1.592316415731741 chr8 146364022 18526657 0.12657931059041272 0.7078712630709346 chr9 141213431 9396569 0.06654160962918605 1.746458199598389 chr10 135534747 14052415 0.10368127222755652 4.649731638478645 chr11 135006516 9721168 0.07200517640200418 0.590906135461505 chr12 133851895 13184878 0.09850348401866107 0.40971966272276583 chr13 115169878 6295383 0.05466171458478058 0.29704736284406574 chr14 107349540 12107237 0.11278331514042818 0.4999738731304071 chr15 102531392 5827597 0.056837197723795654 0.30023655975646646 chr16 90354753 8482151 0.09387609083497798 2.108423852995641 chr17 81195210 6996381 0.08616741061449315 1.2168141784401874 chr18 78077248 11381957 0.14577815293899704 2.058234802482956 chr19 59128983 5643112 0.09543732554980694 0.7841062607067605 chr20 63025520 8302616 0.13173419275239617 0.6074292904500138 chr21 48129895 5193669 0.10790941887573202 0.6249198090287976 chr22 51304566 3040964 0.05927277505865657 0.3884343766275861 chrMT 16571 80206 4.840142417476314 5.600490830771537 chrX 155270560 12843707 0.08271823712106145 0.5392195861264957 chrY 59373566 5430626 0.09146538377027918 2.371084214325662