BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006228.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 = 12,224,110 number of mapped reads = 10,817,744 (88.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,470,901 number of mapped paired reads (second in pair) = 5,346,843 number of mapped paired reads (both in pair) = 9,917,324 number of mapped paired reads (singletons) = 900,420 number of mapped bases = 418,436,504 bp number of sequenced bases = 418,385,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 664,187 duplication rate = 5.38% >>>>>>> Insert size mean insert size = 81,889.7844 std insert size = 2,730,294.0553 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 48.1794 >>>>>>> ACTG content number of A's = 117,546,270 bp (28.1%) number of C's = 89,281,988 bp (21.34%) number of T's = 120,018,970 bp (28.69%) number of G's = 91,520,289 bp (21.87%) number of N's = 17,598 bp (0%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,661,572 number of insertions = 12,075 mapped reads with insertion percentage = 0.11% number of deletions = 38,963 mapped reads with deletion percentage = 0.36% homopolymer indels = 44.67% >>>>>>> Coverage mean coverageData = 0.1352X std coverageData = 0.7162X There is a 10.37% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 34855721 0.1398420628207783 1.0837341844888857 chr2 243199373 36063635 0.14828835516775776 0.6336745340703563 chr3 198022430 28360505 0.14321864952369284 0.46343328042691795 chr4 191154276 26495599 0.13860845571667987 0.5241325875686396 chr5 180915260 24808728 0.13712899619412977 0.4552377251036705 chr6 171115067 23719186 0.13861541485414608 0.5365702232659496 chr7 159138663 22120014 0.13899836521813683 0.8054595865278866 chr8 146364022 21072751 0.14397493804864148 1.6484824203975095 chr9 141213431 17536338 0.12418321597185752 0.5367879878968154 chr10 135534747 20312725 0.1498709773664166 0.7561035156424968 chr11 135006516 18770195 0.13903177088134028 0.6003236076697805 chr12 133851895 19319293 0.14433335441384673 0.47092014586917563 chr13 115169878 13061231 0.11340839485824583 0.413632232309015 chr14 107349540 12422899 0.11572382145279803 0.4805547737043178 chr15 102531392 11979004 0.11683255017156112 0.41803602990224986 chr16 90354753 12699076 0.14054685092216454 0.6041951836551738 chr17 81195210 11206108 0.1380143976473489 0.4872153449153275 chr18 78077248 10701673 0.13706519215431365 0.9738105517068468 chr19 59128983 8644943 0.14620483156289024 0.7847604084392024 chr20 63025520 9297023 0.1475120395674641 0.5000543145933264 chr21 48129895 5517226 0.11463199743111843 0.4965461962334393 chr22 51304566 5249770 0.10232559027982031 0.4069903609167975 chrMT 16571 2878 0.1736769054372096 0.5355142983196322 chrX 155270560 23192402 0.14936767150192543 0.5414958452014977 chrY 59373566 1027581 0.017307045360893433 0.41303252405537727