BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618595.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 = 55,607,778 number of mapped reads = 53,280,888 (95.82%) number of supplementary alignments = 151,543 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,863,795 number of mapped paired reads (second in pair) = 26,417,093 number of mapped paired reads (both in pair) = 52,283,466 number of mapped paired reads (singletons) = 997,422 number of mapped bases = 5,035,541,507 bp number of sequenced bases = 5,032,101,965 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,185,164 duplication rate = 27.86% >>>>>>> Insert size mean insert size = 54,687.0298 std insert size = 2,311,363.5625 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 53.6681 >>>>>>> ACTG content number of A's = 1,393,697,970 bp (27.7%) number of C's = 1,079,530,822 bp (21.45%) number of T's = 1,403,952,739 bp (27.9%) number of G's = 1,154,771,137 bp (22.95%) number of N's = 149,297 bp (0%) GC percentage = 44.4% >>>>>>> Mismatches and indels general error rate = 0.0125 number of mismatches = 61,330,009 number of insertions = 904,655 mapped reads with insertion percentage = 1.67% number of deletions = 2,528,027 mapped reads with deletion percentage = 4.63% homopolymer indels = 53.11% >>>>>>> Coverage mean coverageData = 1.6266X std coverageData = 6.1005X There is a 25.89% of reference with a coverageData >= 1X There is a 18.65% of reference with a coverageData >= 2X There is a 14.48% of reference with a coverageData >= 3X There is a 11.78% of reference with a coverageData >= 4X There is a 9.78% of reference with a coverageData >= 5X There is a 8.28% of reference with a coverageData >= 6X There is a 7.09% of reference with a coverageData >= 7X There is a 6.13% of reference with a coverageData >= 8X There is a 5.35% of reference with a coverageData >= 9X There is a 4.71% of reference with a coverageData >= 10X There is a 4.16% of reference with a coverageData >= 11X There is a 3.7% of reference with a coverageData >= 12X There is a 3.31% of reference with a coverageData >= 13X There is a 2.97% of reference with a coverageData >= 14X There is a 2.67% of reference with a coverageData >= 15X There is a 2.41% of reference with a coverageData >= 16X There is a 2.19% of reference with a coverageData >= 17X There is a 1.99% of reference with a coverageData >= 18X There is a 1.81% of reference with a coverageData >= 19X There is a 1.66% of reference with a coverageData >= 20X There is a 1.52% of reference with a coverageData >= 21X There is a 1.39% of reference with a coverageData >= 22X There is a 1.28% of reference with a coverageData >= 23X There is a 1.18% of reference with a coverageData >= 24X There is a 1.09% of reference with a coverageData >= 25X There is a 1% of reference with a coverageData >= 26X There is a 0.93% of reference with a coverageData >= 27X There is a 0.86% of reference with a coverageData >= 28X There is a 0.8% of reference with a coverageData >= 29X There is a 0.74% of reference with a coverageData >= 30X There is a 0.69% of reference with a coverageData >= 31X There is a 0.64% of reference with a coverageData >= 32X There is a 0.6% of reference with a coverageData >= 33X There is a 0.56% of reference with a coverageData >= 34X There is a 0.52% of reference with a coverageData >= 35X There is a 0.49% of reference with a coverageData >= 36X There is a 0.46% of reference with a coverageData >= 37X There is a 0.43% of reference with a coverageData >= 38X There is a 0.4% of reference with a coverageData >= 39X There is a 0.38% of reference with a coverageData >= 40X There is a 0.35% of reference with a coverageData >= 41X There is a 0.33% of reference with a coverageData >= 42X There is a 0.31% of reference with a coverageData >= 43X There is a 0.29% of reference with a coverageData >= 44X There is a 0.28% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.23% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 430392017 1.726744010800278 7.183876580126003 chr2 243199373 432734420 1.7793401959140742 6.875220858854352 chr3 198022430 333317300 1.6832300260127098 5.392032268040617 chr4 191154276 262990661 1.3758031810912772 5.173227099218553 chr5 180915260 292967385 1.6193624849556638 5.352445371799931 chr6 171115067 279682257 1.6344689097424716 5.444365855257912 chr7 159138663 252149620 1.5844648638275918 5.330468243348212 chr8 146364022 246783548 1.6860943326632551 5.4477583099292 chr9 141213431 215339745 1.5249239642084753 6.702637622499467 chr10 135534747 251723869 1.857264462226797 6.31118288941814 chr11 135006516 256332764 1.8986695723634555 6.50700070196083 chr12 133851895 228843361 1.709675914562136 5.625302462218658 chr13 115169878 134029550 1.163755248572895 4.325972574839009 chr14 107349540 154661405 1.4407272262182027 5.204676449197025 chr15 102531392 161620728 1.5763048257454653 5.536479026361121 chr16 90354753 167213856 1.850637077166267 9.32285338272146 chr17 81195210 155866239 1.9196482033853968 6.5997447524119135 chr18 78077248 125458786 1.606854611474011 6.623853907264276 chr19 59128983 94929600 1.6054664765669993 6.417197808223707 chr20 63025520 140288944 2.2259069659401463 6.964873355306699 chr21 48129895 62854616 1.305937110396771 8.095946102070107 chr22 51304566 82086193 1.599978313821035 6.330402115075064 chrMT 16571 8281 0.49972844125279103 2.2297134354883656 chrX 155270560 266945408 1.7192274440177198 5.456317666589424 chrY 59373566 6320954 0.10646074382663827 3.090937504908596