BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506341.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 = 6,455,333 number of mapped reads = 4,448,649 (68.91%) number of supplementary alignments = 71,820 (1.11%) number of secondary alignments = 0 number of mapped bases = 340,207,040 bp number of sequenced bases = 340,071,412 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 632,205 duplication rate = 10.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3603 >>>>>>> ACTG content number of A's = 94,260,977 bp (27.72%) number of C's = 62,555,934 bp (18.39%) number of T's = 96,886,537 bp (28.49%) number of G's = 86,286,724 bp (25.37%) number of N's = 81,240 bp (0.02%) GC percentage = 43.77% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 2,400,069 number of insertions = 26,993 mapped reads with insertion percentage = 0.59% number of deletions = 68,344 mapped reads with deletion percentage = 1.51% homopolymer indels = 43.57% >>>>>>> Coverage mean coverageData = 0.1099X std coverageData = 0.6904X There is a 6.91% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 24493039 0.09826671204161212 0.8924423251423497 chr2 243199373 26920392 0.11069268669537236 0.7499551181669529 chr3 198022430 22184019 0.11202780917293056 0.49713562322211496 chr4 191154276 19699267 0.10305428375559854 0.659339453542798 chr5 180915260 26013489 0.14378825202473247 0.5723455294507059 chr6 171115067 12898446 0.07537878590200359 0.42784808989265577 chr7 159138663 20746865 0.13036973296677754 1.1683714235193825 chr8 146364022 21813428 0.149035450802247 0.8751693958268634 chr9 141213431 8689144 0.06153199407781545 0.5500196417499166 chr10 135534747 18391683 0.13569718029576577 0.8090121007234347 chr11 135006516 14539238 0.10769286128382129 0.6250735120736705 chr12 133851895 14426410 0.10777889995505854 0.5188619651263838 chr13 115169878 6331853 0.054978377245480804 0.3397768263301146 chr14 107349540 9172048 0.08544096229941926 0.47509108341273754 chr15 102531392 12837099 0.1252016455604153 0.5514423043295246 chr16 90354753 12558183 0.13898751956081382 0.6272230463193244 chr17 81195210 9017589 0.11106060320553392 0.558551975602717 chr18 78077248 5555380 0.07115235414035084 0.8120854346487872 chr19 59128983 8904078 0.15058736931091812 0.8336621506969261 chr20 63025520 9777031 0.15512812904994674 0.642059043247642 chr21 48129895 6168473 0.1281630263269845 0.640367307901765 chr22 51304566 4191051 0.08168962973003221 0.4512414798985933 chrMT 16571 39647 2.392553255687647 2.845578579049324 chrX 155270560 23651652 0.15232541184883985 0.6299522853355303 chrY 59373566 1187536 0.020001089373678515 0.6523932675724795