BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818939.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 5,593,067 number of mapped reads = 5,498,603 (98.31%) number of supplementary alignments = 64,237 (1.15%) number of secondary alignments = 0 number of mapped bases = 510,060,927 bp number of sequenced bases = 509,785,955 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,252,206 duplication rate = 47.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4399 >>>>>>> ACTG content number of A's = 145,966,878 bp (28.63%) number of C's = 112,059,447 bp (21.98%) number of T's = 146,332,835 bp (28.7%) number of G's = 105,403,270 bp (20.68%) number of N's = 23,525 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 3,311,204 number of insertions = 58,935 mapped reads with insertion percentage = 1.05% number of deletions = 152,211 mapped reads with deletion percentage = 2.71% homopolymer indels = 43.78% >>>>>>> Coverage mean coverageData = 0.1648X std coverageData = 1.6879X There is a 5.05% of reference with a coverageData >= 1X There is a 3.1% of reference with a coverageData >= 2X There is a 2.14% of reference with a coverageData >= 3X There is a 1.52% of reference with a coverageData >= 4X There is a 1.1% of reference with a coverageData >= 5X There is a 0.8% of reference with a coverageData >= 6X There is a 0.59% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 61242182 0.24570523336830524 3.132921609502261 chr2 243199373 44817840 0.18428435668705445 2.202703269713491 chr3 198022430 33904066 0.17121326104320606 1.0220858245884115 chr4 191154276 33305512 0.17423367500290707 1.1491588953668326 chr5 180915260 26005681 0.14374509369745814 0.9544473862002014 chr6 171115067 27355740 0.15986751184219214 1.1098427424546777 chr7 159138663 25678808 0.16136121490476515 1.4764922785672663 chr8 146364022 33502116 0.22889584162971416 1.4923676343537933 chr9 141213431 19143197 0.13556215484913756 2.064473719139454 chr10 135534747 24910391 0.18379339284855123 2.0374853618311235 chr11 135006516 19567658 0.14493861911079906 1.2322761964076718 chr12 133851895 22814454 0.1704455062066921 1.0394190256744362 chr13 115169878 8255252 0.07167891590542451 0.6370950374403908 chr14 107349540 12330086 0.11485923460873702 0.9709307789127879 chr15 102531392 14884480 0.14516997877098947 0.9528453778007373 chr16 90354753 15333407 0.16970227343767957 1.5403453311005875 chr17 81195210 11075748 0.13640888421866265 1.0727975873959759 chr18 78077248 12706468 0.16274226263712574 2.7351836193617602 chr19 59128983 8067313 0.13643584906576187 2.6704868166818665 chr20 63025520 11431891 0.18138511193560958 1.1385241297234445 chr21 48129895 6852889 0.14238321109987878 1.0795205080326946 chr22 51304566 6305101 0.122895513822298 0.9402375120468678 chrMT 16571 32911 1.9860599843099391 3.7432188267071287 chrX 155270560 29085617 0.18732216203767152 1.4994822765447668 chrY 59373566 1452119 0.02445733173580984 1.1530519381722384