BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004064.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,875,645 number of mapped reads = 2,067,542 (71.9%) number of supplementary alignments = 20,236 (0.7%) number of secondary alignments = 0 number of mapped bases = 133,946,017 bp number of sequenced bases = 133,886,680 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 367,625 duplication rate = 12.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5701 >>>>>>> ACTG content number of A's = 37,439,097 bp (27.96%) number of C's = 24,253,120 bp (18.11%) number of T's = 42,857,072 bp (32.01%) number of G's = 29,235,299 bp (21.84%) number of N's = 102,092 bp (0.08%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,138,283 number of insertions = 9,915 mapped reads with insertion percentage = 0.48% number of deletions = 35,348 mapped reads with deletion percentage = 1.69% homopolymer indels = 46.67% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.5248X There is a 1.75% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% 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 9667441 0.038786025732710214 0.48049646240341315 chr2 243199373 5555563 0.02284365675564468 0.4196296811006163 chr3 198022430 11416512 0.057652620463247525 0.5140159664924221 chr4 191154276 10412133 0.05446978858061224 0.5303694419389792 chr5 180915260 9898997 0.0547162080191577 0.505472848047568 chr6 171115067 5490736 0.03208797504663923 0.3917995543941289 chr7 159138663 12863039 0.0808291257291762 1.117321835800113 chr8 146364022 6843380 0.04675588923075645 0.6036895695094219 chr9 141213431 1712768 0.012128931277082276 0.25194665579491765 chr10 135534747 5266167 0.038854737375943894 0.4416701192652129 chr11 135006516 3125497 0.02315071222191972 0.335007952240372 chr12 133851895 10132913 0.07570242468364008 0.5855779708135895 chr13 115169878 11301609 0.09812990337629775 0.6929435986448578 chr14 107349540 6382384 0.05945422774983479 0.5357413195828055 chr15 102531392 1123133 0.010954040300164851 0.40520394278446653 chr16 90354753 7923781 0.08769633845382765 0.6403887975243794 chr17 81195210 2076222 0.025570744875221086 0.33359541707285506 chr18 78077248 1294159 0.016575366488327047 0.5345781411542063 chr19 59128983 3133344 0.05299167753316508 0.4999428777736597 chr20 63025520 2956392 0.04690785573843738 0.45439298951075413 chr21 48129895 846089 0.01757928206575144 0.27703481034999217 chr22 51304566 1445926 0.028183183539648302 0.33616493023801963 chrMT 16571 57698 3.481865910325267 4.0782561401055695 chrX 155270560 2779605 0.017901687222613226 0.28440501920901307 chrY 59373566 240529 0.004051112577607348 0.17335861966852154