BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618633.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 = 22,158,324 number of mapped reads = 20,839,378 (94.05%) number of supplementary alignments = 99,985 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,647,208 number of mapped paired reads (second in pair) = 10,192,170 number of mapped paired reads (both in pair) = 20,197,046 number of mapped paired reads (singletons) = 642,332 number of mapped bases = 1,956,672,752 bp number of sequenced bases = 1,955,230,510 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,445,163 duplication rate = 18.57% >>>>>>> Insert size mean insert size = 109,120.063 std insert size = 3,295,591.5039 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 53.354 >>>>>>> ACTG content number of A's = 539,007,926 bp (27.57%) number of C's = 418,253,171 bp (21.39%) number of T's = 548,842,160 bp (28.07%) number of G's = 449,054,286 bp (22.97%) number of N's = 72,967 bp (0%) GC percentage = 44.36% >>>>>>> Mismatches and indels general error rate = 0.0125 number of mismatches = 23,905,220 number of insertions = 372,353 mapped reads with insertion percentage = 1.76% number of deletions = 1,059,232 mapped reads with deletion percentage = 4.95% homopolymer indels = 52.97% >>>>>>> Coverage mean coverageData = 0.6321X std coverageData = 2.6151X There is a 20.12% of reference with a coverageData >= 1X There is a 11.9% of reference with a coverageData >= 2X There is a 7.69% of reference with a coverageData >= 3X There is a 5.35% of reference with a coverageData >= 4X There is a 3.83% of reference with a coverageData >= 5X There is a 2.83% of reference with a coverageData >= 6X There is a 2.13% of reference with a coverageData >= 7X There is a 1.64% of reference with a coverageData >= 8X There is a 1.28% of reference with a coverageData >= 9X There is a 1.01% of reference with a coverageData >= 10X There is a 0.8% of reference with a coverageData >= 11X There is a 0.65% of reference with a coverageData >= 12X There is a 0.52% of reference with a coverageData >= 13X There is a 0.43% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% 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 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 170562415 0.6843008627850119 3.25522513589763 chr2 243199373 165153470 0.6790867425468239 3.1269034518270447 chr3 198022430 129617631 0.6545603495523209 2.216104902773641 chr4 191154276 103693995 0.5424623355011948 2.1454592249650504 chr5 180915260 111729059 0.6175767538901915 2.193623936176539 chr6 171115067 106691855 0.6235094131132239 2.1515336183137275 chr7 159138663 98136144 0.616670657840075 2.202690654448541 chr8 146364022 95815255 0.654636663373462 2.405725754467663 chr9 141213431 83166400 0.58894114682335 2.846945736477124 chr10 135534747 96099882 0.7090423978140454 2.4208464958971208 chr11 135006516 97214963 0.7200760813648431 2.8070579570618857 chr12 133851895 88155927 0.658607986087907 2.4612465630550258 chr13 115169878 53613697 0.4655183970933789 1.7462366007448429 chr14 107349540 59278148 0.5521975035943331 2.0785285467737675 chr15 102531392 62210455 0.6067454443610792 2.267159725009618 chr16 90354753 65760915 0.727808032411975 4.784875334817333 chr17 81195210 61835401 0.7615646415595205 2.4906427932893704 chr18 78077248 49872966 0.6387643939499507 2.9326370384580156 chr19 59128983 40052096 0.6773682544142523 2.6504176251527034 chr20 63025520 53146230 0.8432493694617672 2.666275178985991 chr21 48129895 24719533 0.5136003932690898 3.0648443339726206 chr22 51304566 32885997 0.6409955207495567 2.4723972434284747 chrMT 16571 7309 0.44107175185565145 1.6714446367586369 chrX 155270560 104249017 0.6714023379576914 2.235245526029945 chrY 59373566 3003992 0.05059477141730042 1.7270191637674868