BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472711.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,216,496 number of mapped reads = 18,004,163 (98.83%) number of supplementary alignments = 55,098 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,046,844 number of mapped paired reads (second in pair) = 8,957,319 number of mapped paired reads (both in pair) = 17,876,174 number of mapped paired reads (singletons) = 127,989 number of mapped bases = 1,772,559,854 bp number of sequenced bases = 1,772,314,817 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,294,909 duplication rate = 47.77% >>>>>>> Insert size mean insert size = 28,883.8757 std insert size = 1,742,294.7945 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 55.1299 >>>>>>> ACTG content number of A's = 478,365,793 bp (26.99%) number of C's = 409,812,865 bp (23.12%) number of T's = 475,610,800 bp (26.84%) number of G's = 408,187,187 bp (23.03%) number of N's = 338,172 bp (0.02%) GC percentage = 46.15% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 10,563,641 number of insertions = 96,362 mapped reads with insertion percentage = 0.53% number of deletions = 96,262 mapped reads with deletion percentage = 0.53% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.5726X std coverageData = 17.2356X There is a 5.14% of reference with a coverageData >= 1X There is a 2.22% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 248622275 0.9974790594403373 28.03102030200752 chr2 243199373 142202437 0.5847154753972166 16.59342326183802 chr3 198022430 187330079 0.9460043440533479 21.532314137739927 chr4 191154276 47266011 0.24726630232430688 8.35053248946505 chr5 180915260 57970189 0.32042730392118385 9.5998146917371 chr6 171115067 135552507 0.792171661891118 21.034067397630977 chr7 159138663 64879724 0.4076930318309888 10.806101044048999 chr8 146364022 90074098 0.6154114704500263 18.2095011831155 chr9 141213431 119035892 0.8429502148418163 22.57037106672477 chr10 135534747 45727805 0.337388057396086 10.820074709121084 chr11 135006516 63582411 0.47095809064504707 14.947059064758644 chr12 133851895 82155930 0.6137823450314245 15.74236288713596 chr13 115169878 40537300 0.35197831849748074 11.83250104722035 chr14 107349540 39494595 0.3679065136189685 12.094528656311228 chr15 102531392 45059503 0.439470313638188 14.15555935919271 chr16 90354753 61604157 0.6818031697790153 15.81255141302588 chr17 81195210 83103658 1.0235044407176237 21.29074557004831 chr18 78077248 31058273 0.39778903324051584 16.992277885831268 chr19 59128983 49714526 0.8407810092049106 21.48465116001502 chr20 63025520 36390043 0.5773858430680143 25.016765455572358 chr21 48129895 7854214 0.16318784821782803 10.127709601815566 chr22 51304566 19671359 0.3834231635445469 9.427979373648682 chrMT 16571 2849 0.17192686017741837 0.6004836008638663 chrX 155270560 69247272 0.4459781171652888 13.775590590268612 chrY 59373566 4422747 0.07449016958152724 3.732137999212237