BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472382.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 = 19,766,942 number of mapped reads = 19,555,461 (98.93%) number of supplementary alignments = 72,780 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,807,170 number of mapped paired reads (second in pair) = 9,748,291 number of mapped paired reads (both in pair) = 19,445,640 number of mapped paired reads (singletons) = 109,821 number of mapped bases = 1,915,092,679 bp number of sequenced bases = 1,914,842,007 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,484,689 duplication rate = 47.66% >>>>>>> Insert size mean insert size = 18,545.3779 std insert size = 1,373,904.9218 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 54.8306 >>>>>>> ACTG content number of A's = 516,681,740 bp (26.98%) number of C's = 442,501,991 bp (23.11%) number of T's = 517,620,610 bp (27.03%) number of G's = 437,800,254 bp (22.86%) number of N's = 237,412 bp (0.01%) GC percentage = 45.97% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 10,586,331 number of insertions = 110,125 mapped reads with insertion percentage = 0.56% number of deletions = 95,901 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.27% >>>>>>> Coverage mean coverageData = 0.6186X std coverageData = 19.3997X There is a 5.52% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.73% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171468992 0.6879380733819717 19.95851024851785 chr2 243199373 180398930 0.7417738285040727 21.73862710203368 chr3 198022430 128627424 0.6495598705661778 13.951375766014367 chr4 191154276 60253667 0.31520962157289123 11.527867609399015 chr5 180915260 68911469 0.3809046787982396 13.25648671684102 chr6 171115067 174933448 1.0223146977466337 34.14551754324422 chr7 159138663 173904264 1.0927844982586035 30.05941872199465 chr8 146364022 98124741 0.6704157186934915 19.348894473648894 chr9 141213431 64096745 0.4538997781308777 10.632241674477903 chr10 135534747 50099077 0.3696400967937764 10.311068911865716 chr11 135006516 56650858 0.4196157317325336 12.65382554843774 chr12 133851895 77044579 0.5755957283981672 15.591021572853997 chr13 115169878 74796922 0.6494486518428022 23.946284631428266 chr14 107349540 28544382 0.265901297760568 7.915113019430839 chr15 102531392 30381440 0.2963135426855416 9.7046916012013 chr16 90354753 99228724 1.0982125533562135 26.458926514287814 chr17 81195210 96138530 1.1840418911411152 27.535061598291946 chr18 78077248 26936257 0.3449949593510263 14.843176967908546 chr19 59128983 49273355 0.8333198458698334 16.900895790908987 chr20 63025520 68343392 1.0843764874926856 29.84269797705845 chr21 48129895 14042484 0.29176219894101163 13.62033367672694 chr22 51304566 10755372 0.2096377152863938 5.09080191855688 chrMT 16571 6849 0.41331241325206686 0.7639129850960107 chrX 155270560 111839265 0.7202863504839553 20.383900519425477 chrY 59373566 291513 0.004909811211272033 0.2612348162290542