BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506124.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 12,624,038 number of mapped reads = 9,393,155 (74.41%) number of supplementary alignments = 122,317 (0.97%) number of secondary alignments = 0 number of mapped bases = 764,343,595 bp number of sequenced bases = 764,028,455 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,761,803 duplication rate = 12.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2122 >>>>>>> ACTG content number of A's = 210,115,790 bp (27.5%) number of C's = 145,852,642 bp (19.09%) number of T's = 218,345,814 bp (28.58%) number of G's = 189,586,874 bp (24.81%) number of N's = 127,335 bp (0.02%) GC percentage = 43.9% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 5,867,114 number of insertions = 61,764 mapped reads with insertion percentage = 0.64% number of deletions = 152,394 mapped reads with deletion percentage = 1.59% homopolymer indels = 43.27% >>>>>>> Coverage mean coverageData = 0.2469X std coverageData = 1.5764X There is a 12.23% of reference with a coverageData >= 1X There is a 5.2% of reference with a coverageData >= 2X There is a 2.64% of reference with a coverageData >= 3X There is a 1.48% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.55% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 58493935 0.23467919464080292 2.929028172492945 chr2 243199373 62438979 0.25673988476935755 1.716705967378871 chr3 198022430 49701112 0.2509872846222521 0.9073485820992105 chr4 191154276 46205966 0.24172080775216348 1.4668155107376366 chr5 180915260 58476898 0.3232281124323067 1.0601042239010543 chr6 171115067 28902880 0.16890903008558564 0.8392371227638724 chr7 159138663 40807459 0.25642705694969925 1.5507249110433556 chr8 146364022 47710883 0.32597411814769617 1.822030345675254 chr9 141213431 20782466 0.147170604473168 1.5785768617234004 chr10 135534747 43946417 0.3242446529228405 2.028994973113479 chr11 135006516 33877363 0.25093131801134694 1.3883305889763844 chr12 133851895 31335082 0.23410264008589493 0.8940070974880491 chr13 115169878 15162738 0.13165541427420804 0.6377667269374133 chr14 107349540 21519766 0.20046444539957972 0.9379458517354669 chr15 102531392 28530626 0.27826234915449116 0.9896340177246108 chr16 90354753 26967717 0.29846484113569544 1.2878769751911463 chr17 81195210 19527808 0.24050443369750507 1.0887664034783373 chr18 78077248 12371452 0.1584514351735348 2.2617291859366646 chr19 59128983 20292552 0.3431912908091113 2.1521679643884384 chr20 63025520 20854424 0.330888567043953 1.1868162517162146 chr21 48129895 13197770 0.2742114853980047 1.3994119426656761 chr22 51304566 9330448 0.18186389102287698 0.8427896065197752 chrMT 16571 556780 33.5996620602257 20.197574736183007 chrX 155270560 50526409 0.32540881542515204 1.1918662705042724 chrY 59373566 2825665 0.04759129677338228 1.6186980491951846