BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063581.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 = 2,572,806 number of mapped reads = 2,109,651 (82%) number of supplementary alignments = 23,596 (0.92%) number of secondary alignments = 0 number of mapped bases = 139,484,175 bp number of sequenced bases = 139,429,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 227,771 duplication rate = 8.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.5874 >>>>>>> ACTG content number of A's = 39,506,303 bp (28.33%) number of C's = 26,167,033 bp (18.77%) number of T's = 43,608,616 bp (31.28%) number of G's = 30,067,799 bp (21.56%) number of N's = 80,226 bp (0.06%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,178,494 number of insertions = 9,692 mapped reads with insertion percentage = 0.46% number of deletions = 33,727 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.0451X std coverageData = 0.4141X There is a 2.36% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% 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 0.01% 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% 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 8900336 0.035708380441708105 0.35546776374191946 chr2 243199373 22700106 0.09333949228561539 0.620109950562841 chr3 198022430 37339419 0.1885615634552106 0.7639261483105625 chr4 191154276 2911174 0.015229447443801884 0.21687770286839403 chr5 180915260 1508967 0.008340739194692586 0.15100346618726446 chr6 171115067 8569901 0.05008267915998303 0.3950205683553585 chr7 159138663 5387605 0.03385478361094438 0.34162164667298944 chr8 146364022 3604658 0.024628033247132277 0.42870679362385194 chr9 141213431 3198393 0.022649354083040443 0.2666997031558507 chr10 135534747 7769170 0.05732234848971976 0.4841202518418881 chr11 135006516 10431993 0.077270292642764 0.5323368043409096 chr12 133851895 3090892 0.023091880768665994 0.2687213101328591 chr13 115169878 1040895 0.009037910068811569 0.1571125605483354 chr14 107349540 760957 0.007088591157446972 0.2587737615252651 chr15 102531392 709735 0.006922123909134092 0.20564303034082168 chr16 90354753 3630263 0.040177886380808325 0.3577832164279217 chr17 81195210 3031741 0.03733891445074161 0.36677678334370123 chr18 78077248 1305729 0.016723553063755527 0.5758003470126041 chr19 59128983 576678 0.009752882101828134 0.26353356551997337 chr20 63025520 1763845 0.027986203049177538 0.31069220483533166 chr21 48129895 4040899 0.0839581927199301 0.5020008686881396 chr22 51304566 953395 0.018583043856174517 0.21871450338890241 chrMT 16571 82495 4.978275300223282 4.663159927375368 chrX 155270560 5921562 0.03813705573033291 0.3608089351102934 chrY 59373566 253367 0.004267336747130869 0.0998515994479912