BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618634.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 36,528,284 number of mapped reads = 24,117,144 (66.02%) number of supplementary alignments = 160,382 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,972,414 number of mapped paired reads (second in pair) = 11,144,730 number of mapped paired reads (both in pair) = 21,023,500 number of mapped paired reads (singletons) = 3,093,644 number of mapped bases = 2,215,810,697 bp number of sequenced bases = 2,214,259,005 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,468,564 duplication rate = 29.74% >>>>>>> Insert size mean insert size = 197,354.2774 std insert size = 4,445,832.0559 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.0963 >>>>>>> ACTG content number of A's = 606,433,732 bp (27.39%) number of C's = 481,072,070 bp (21.73%) number of T's = 626,437,111 bp (28.29%) number of G's = 499,123,188 bp (22.54%) number of N's = 1,192,904 bp (0.05%) GC percentage = 44.27% >>>>>>> Mismatches and indels general error rate = 0.0151 number of mismatches = 32,758,393 number of insertions = 434,109 mapped reads with insertion percentage = 1.77% number of deletions = 1,126,106 mapped reads with deletion percentage = 4.55% homopolymer indels = 51.62% >>>>>>> Coverage mean coverageData = 0.7158X std coverageData = 4.6656X There is a 18.77% of reference with a coverageData >= 1X There is a 11.78% of reference with a coverageData >= 2X There is a 8.13% of reference with a coverageData >= 3X There is a 5.99% of reference with a coverageData >= 4X There is a 4.52% of reference with a coverageData >= 5X There is a 3.52% of reference with a coverageData >= 6X There is a 2.77% of reference with a coverageData >= 7X There is a 2.22% of reference with a coverageData >= 8X There is a 1.8% of reference with a coverageData >= 9X There is a 1.47% of reference with a coverageData >= 10X There is a 1.21% of reference with a coverageData >= 11X There is a 1% of reference with a coverageData >= 12X There is a 0.84% of reference with a coverageData >= 13X There is a 0.7% of reference with a coverageData >= 14X There is a 0.59% of reference with a coverageData >= 15X There is a 0.51% of reference with a coverageData >= 16X There is a 0.43% of reference with a coverageData >= 17X There is a 0.37% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.16% of reference with a coverageData >= 24X There is a 0.15% of reference with a coverageData >= 25X There is a 0.13% of reference with a coverageData >= 26X There is a 0.12% of reference with a coverageData >= 27X There is a 0.1% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.08% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192437671 0.7720649610738582 4.553186350291512 chr2 243199373 189716982 0.7800882858361645 7.029164995940565 chr3 198022430 145992537 0.7372525274030826 3.925592857491393 chr4 191154276 118462014 0.6197194040273523 4.094114757006577 chr5 180915260 130753914 0.7227356829932422 4.1966204702732295 chr6 171115067 122384953 0.7152202032565607 3.524694533220176 chr7 159138663 111663810 0.701676185378031 4.446378132835191 chr8 146364022 110190710 0.7528537990025992 5.0167037261491 chr9 141213431 94295276 0.667750052755251 4.650482797056861 chr10 135534747 110038960 0.8118874490539315 5.728052418378376 chr11 135006516 109757961 0.8129826933686667 4.559063095737835 chr12 133851895 101011720 0.754652894529435 6.521908620373187 chr13 115169878 62054814 0.5388111464353552 3.207652674161135 chr14 107349540 68065709 0.6340568296799409 4.240832689397442 chr15 102531392 71564027 0.6979718660212865 3.6152067517685262 chr16 90354753 73936901 0.8182956462733068 6.321880423957461 chr17 81195210 65977746 0.8125817520516296 3.9551438066813525 chr18 78077248 57483527 0.7362391538185362 3.980178308760786 chr19 59128983 39666485 0.6708467317964864 3.372363363026493 chr20 63025520 58316241 0.925279807290761 3.4783850317644314 chr21 48129895 27791918 0.5774356665436315 3.494335935684642 chr22 51304566 35382693 0.6896597273622781 4.530942495267532 chrMT 16571 18902 1.1406674310542515 4.721129487635648 chrX 155270560 114804469 0.7393833641097192 3.3657215849065656 chrY 59373566 4040757 0.0680564984087363 2.4391630911634086