BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006028.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 13,103,140 number of mapped reads = 8,188,168 (62.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,156,065 number of mapped paired reads (second in pair) = 4,032,103 number of mapped paired reads (both in pair) = 6,983,796 number of mapped paired reads (singletons) = 1,204,372 number of mapped bases = 315,994,521 bp number of sequenced bases = 315,959,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 271,784 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 72,498.9555 std insert size = 2,596,181.9529 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 46.7769 >>>>>>> ACTG content number of A's = 94,650,643 bp (29.96%) number of C's = 63,859,598 bp (20.21%) number of T's = 92,717,626 bp (29.34%) number of G's = 64,614,342 bp (20.45%) number of N's = 117,402 bp (0.04%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 2,430,699 number of insertions = 9,257 mapped reads with insertion percentage = 0.11% number of deletions = 27,446 mapped reads with deletion percentage = 0.34% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.1021X std coverageData = 0.568X There is a 7.63% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% 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 25408118 0.10193803288458006 0.7550109740124796 chr2 243199373 28062273 0.11538793317530469 0.5451981078330085 chr3 198022430 22189051 0.11205322043568498 0.42005098534650614 chr4 191154276 21782853 0.11395430672971187 0.4704562397842692 chr5 180915260 19254494 0.10642824712520105 0.4092953740107906 chr6 171115067 19798125 0.11570065305821374 0.5235945939704564 chr7 159138663 17042595 0.10709273710562718 0.6118514262635047 chr8 146364022 16496744 0.11271037632458611 1.2557219671030053 chr9 141213431 12463447 0.0882596429513847 0.4486032123428819 chr10 135534747 15124396 0.11159054290336337 0.6637243244854855 chr11 135006516 13707163 0.10152964024343833 0.4638286178529122 chr12 133851895 14469653 0.1081019659826258 0.4161835777888648 chr13 115169878 10778131 0.09358463503799144 0.38413325473412824 chr14 107349540 9215173 0.08584268735571667 0.3942248996450578 chr15 102531392 8500302 0.08290438502970876 0.3618643898535386 chr16 90354753 8240449 0.09120105723713284 0.45901323054617 chr17 81195210 7476515 0.09208073973821855 0.40166281617015354 chr18 78077248 8841309 0.11323796914563382 0.6804876153450111 chr19 59128983 5296748 0.08957955525803649 0.5938765991245 chr20 63025520 6033698 0.09573420417634 0.4051276495524655 chr21 48129895 4038031 0.08389860397576185 0.4143369749316667 chr22 51304566 3051602 0.059480125024349684 0.30770158244309215 chrMT 16571 79844 4.818297024923059 3.9299406820188745 chrX 155270560 17852721 0.114978145245306 0.46420258925271646 chrY 59373566 791086 0.013323875476840991 0.27161515952572535