BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068947.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 = 2,287,506 number of mapped reads = 1,751,365 (76.56%) number of supplementary alignments = 13,370 (0.58%) number of secondary alignments = 0 number of mapped bases = 116,545,321 bp number of sequenced bases = 116,495,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,834 duplication rate = 4.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6075 >>>>>>> ACTG content number of A's = 32,283,778 bp (27.71%) number of C's = 20,256,373 bp (17.39%) number of T's = 38,527,734 bp (33.07%) number of G's = 25,142,874 bp (21.58%) number of N's = 284,548 bp (0.24%) GC percentage = 38.97% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,133,311 number of insertions = 9,980 mapped reads with insertion percentage = 0.57% number of deletions = 30,650 mapped reads with deletion percentage = 1.73% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.3707X There is a 2.98% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 10722552 0.043019158616258775 0.6275671847829052 chr2 243199373 16239520 0.06677451425830773 0.38099927691763474 chr3 198022430 10629586 0.05367869690317405 0.2813920240314168 chr4 191154276 10578143 0.05533824940437116 0.28709341531143895 chr5 180915260 1196973 0.006616208052322397 0.09269899814790024 chr6 171115067 14206511 0.08302314488764452 0.4200687169863482 chr7 159138663 8392055 0.0527342309015126 0.7232037996049205 chr8 146364022 11689315 0.07986467466711183 0.651755152564856 chr9 141213431 1495655 0.010591450044153378 0.21970300723420294 chr10 135534747 7095971 0.05235536389793829 0.3419486275995599 chr11 135006516 1144496 0.00847733897525361 0.17708814640095188 chr12 133851895 2258695 0.01687458365830383 0.1575133527649772 chr13 115169878 1956419 0.016987245571276892 0.15696778072952655 chr14 107349540 7593911 0.070740042295477 0.33268694372752977 chr15 102531392 2105649 0.020536627455521133 0.17378901026594415 chr16 90354753 860559 0.009524225028870369 0.12769314260787393 chr17 81195210 461337 0.005681825319498527 0.08245717737722072 chr18 78077248 1327934 0.01700795089499056 0.4536398264082774 chr19 59128983 1367743 0.02313151572385407 0.3177327069905401 chr20 63025520 722168 0.011458342588843377 0.1289812457487249 chr21 48129895 731135 0.015190870455877787 0.1503910104149349 chr22 51304566 308827 0.0060194837239243 0.09347803107315726 chrMT 16571 113879 6.872186349646974 4.652842528925968 chrX 155270560 3179848 0.020479400602406536 0.17972568311603762 chrY 59373566 166440 0.002803267703341248 0.07496327761656174