BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472839.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 = 2,981,744 number of mapped reads = 2,537,307 (85.09%) number of supplementary alignments = 19,485 (0.65%) number of secondary alignments = 0 number of mapped bases = 164,870,835 bp number of sequenced bases = 164,808,189 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,603 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9886 >>>>>>> ACTG content number of A's = 44,388,961 bp (26.93%) number of C's = 32,649,201 bp (19.81%) number of T's = 49,031,951 bp (29.75%) number of G's = 38,734,229 bp (23.5%) number of N's = 3,847 bp (0%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,394,676 number of insertions = 12,495 mapped reads with insertion percentage = 0.49% number of deletions = 34,982 mapped reads with deletion percentage = 1.36% homopolymer indels = 45.29% >>>>>>> Coverage mean coverageData = 0.0533X std coverageData = 0.3469X There is a 4.57% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 11907432 0.047772928116395746 0.43638408855679456 chr2 243199373 16397381 0.06742361543835065 0.5026313649381636 chr3 198022430 12986346 0.06558017695268158 0.28915456536336265 chr4 191154276 9406811 0.04921057062830234 0.2751624214573496 chr5 180915260 8178987 0.04520893925697589 0.23946457459040166 chr6 171115067 10600933 0.061952072285954805 0.3035519821065105 chr7 159138663 9402154 0.059081519366541366 0.3834738195446467 chr8 146364022 8962648 0.061235321888052516 0.3719771448456168 chr9 141213431 9445406 0.06688744783773436 0.39702031887023803 chr10 135534747 6323762 0.046657865528756254 0.33497059493196674 chr11 135006516 6263295 0.04639253856458306 0.3285936057156701 chr12 133851895 7289027 0.05445591188679099 0.2697200530530138 chr13 115169878 6681141 0.05801118413965846 0.28104979424426535 chr14 107349540 3354730 0.03125052981130613 0.2305962570391878 chr15 102531392 2925065 0.02852848228179717 0.2054582492097 chr16 90354753 5361343 0.05933659073806555 0.3026746021458632 chr17 81195210 3543539 0.04364221731799203 0.2490784944589478 chr18 78077248 2886901 0.036974932825501225 0.6258361999381602 chr19 59128983 3817334 0.06455943948841468 0.3802469070334417 chr20 63025520 6281304 0.09966286672446337 0.3743037251940775 chr21 48129895 2359261 0.0490186193009563 0.2835262658021228 chr22 51304566 1785805 0.0348079155371863 0.22239089543939974 chrMT 16571 21023 1.2686621205720838 1.4494107191589554 chrX 155270560 7918900 0.051000653311226544 0.2769974726159444 chrY 59373566 770307 0.01297390491923628 0.1721331968600828