BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082422.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,112,561 number of mapped reads = 2,757,139 (88.58%) number of supplementary alignments = 26,713 (0.86%) number of secondary alignments = 0 number of mapped bases = 185,497,371 bp number of sequenced bases = 185,432,111 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,170 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4255 >>>>>>> ACTG content number of A's = 51,882,849 bp (27.98%) number of C's = 34,432,422 bp (18.57%) number of T's = 58,328,051 bp (31.46%) number of G's = 40,784,974 bp (21.99%) number of N's = 3,815 bp (0%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,553,306 number of insertions = 14,817 mapped reads with insertion percentage = 0.53% number of deletions = 40,725 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.79% >>>>>>> Coverage mean coverageData = 0.0599X std coverageData = 0.5012X There is a 5.09% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 14568201 0.058448002823631884 0.8763968860426508 chr2 243199373 15846060 0.06515666469255248 0.6338991018504455 chr3 198022430 12586771 0.06356234998227221 0.2846770997027714 chr4 191154276 12521182 0.06550301809623134 0.30149212782581075 chr5 180915260 11450129 0.06329001213054111 0.288293907850153 chr6 171115067 10985122 0.06419728076896934 0.366242319759924 chr7 159138663 10043643 0.0631125259610859 0.6874098367542769 chr8 146364022 9757186 0.06666382808201321 0.8577585181152285 chr9 141213431 7969808 0.056438031025533256 0.4385457767130986 chr10 135534747 8681976 0.06405719708171957 0.41179083366387637 chr11 135006516 8466962 0.06271520998290186 0.41978718586649033 chr12 133851895 8485541 0.06339500087017819 0.2922379770000502 chr13 115169878 6150690 0.05340537045632713 0.26267100275701866 chr14 107349540 5629157 0.05243764435320356 0.2775275864861432 chr15 102531392 4995727 0.048723877658853984 0.2594065258882177 chr16 90354753 4862140 0.05381166832474214 0.29361119594090024 chr17 81195210 4740370 0.058382384872211056 0.30812943274189547 chr18 78077248 5065824 0.06488220486459768 0.8153705355694042 chr19 59128983 3265961 0.055234520099897544 0.67814377524975 chr20 63025520 3601142 0.057137838767534165 0.2770189064484526 chr21 48129895 2409378 0.050059905595056874 0.27179442133991205 chr22 51304566 1861381 0.036281000798252534 0.2138287123006408 chrMT 16571 8950 0.540100175004526 0.7865728024709225 chrX 155270560 11088967 0.071417060645624 0.34655514426615985 chrY 59373566 455103 0.007665077755309492 0.15465314327857071