BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236098.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 = 3,749,792 number of mapped reads = 3,212,015 (85.66%) number of supplementary alignments = 21,758 (0.58%) number of secondary alignments = 0 number of mapped bases = 199,468,652 bp number of sequenced bases = 199,373,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 237,504 duplication rate = 5.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1417 >>>>>>> ACTG content number of A's = 56,495,254 bp (28.34%) number of C's = 35,584,583 bp (17.85%) number of T's = 63,874,354 bp (32.04%) number of G's = 43,348,899 bp (21.74%) number of N's = 70,131 bp (0.04%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,745,331 number of insertions = 15,257 mapped reads with insertion percentage = 0.47% number of deletions = 56,911 mapped reads with deletion percentage = 1.75% homopolymer indels = 44.96% >>>>>>> Coverage mean coverageData = 0.0644X std coverageData = 0.6381X There is a 4.95% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 16954253 0.0680209057533301 0.8064465503170152 chr2 243199373 14705493 0.060466821187076004 0.6505709542635522 chr3 198022430 16124501 0.08142764938295122 0.35949210266802917 chr4 191154276 11254005 0.05887393803317274 0.3847860063002779 chr5 180915260 11341234 0.06268810049522633 0.3170831302288858 chr6 171115067 21322664 0.12461009058892517 0.6617535114725415 chr7 159138663 10327833 0.06489832706461786 0.6504597258246725 chr8 146364022 12745934 0.08708379167115263 1.9083459052060614 chr9 141213431 8406878 0.05953313321875169 0.450684347003744 chr10 135534747 7246215 0.05346389144032563 0.49110882942281375 chr11 135006516 7252276 0.05371797017560249 0.4136445980782457 chr12 133851895 6433563 0.04806478832443874 0.28931611655643075 chr13 115169878 8402228 0.07295508292541562 0.35158888911323166 chr14 107349540 4978591 0.04637738550160532 0.29802836789272263 chr15 102531392 4939961 0.0481799856964782 0.29361756220975277 chr16 90354753 3894100 0.04309789879011677 0.2927792095476608 chr17 81195210 4141972 0.05101251662505707 0.3219164383243213 chr18 78077248 5680229 0.07275139871733184 0.7575099426569144 chr19 59128983 3371124 0.05701305567863395 0.5433747933605928 chr20 63025520 2948066 0.0467757505213761 0.2868793294424574 chr21 48129895 3553874 0.07383922196381272 0.37827805590577906 chr22 51304566 1902559 0.03708361941898115 0.23337613902153814 chrMT 16571 84864 5.121235894031742 4.22292932450607 chrX 155270560 10937097 0.07043896151337381 0.36864979062145925 chrY 59373566 519138 0.008743588013561456 0.23934455830343845