BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080634.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 = 3,197,868 number of mapped reads = 2,706,423 (84.63%) number of supplementary alignments = 21,342 (0.67%) number of secondary alignments = 0 number of mapped bases = 178,644,881 bp number of sequenced bases = 178,573,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,723 duplication rate = 4.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8879 >>>>>>> ACTG content number of A's = 48,887,907 bp (27.38%) number of C's = 31,178,528 bp (17.46%) number of T's = 58,815,259 bp (32.94%) number of G's = 39,546,087 bp (22.15%) number of N's = 145,837 bp (0.08%) GC percentage = 39.61% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,569,572 number of insertions = 14,358 mapped reads with insertion percentage = 0.53% number of deletions = 43,739 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.76% >>>>>>> Coverage mean coverageData = 0.0577X std coverageData = 0.4247X There is a 4.74% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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 20787798 0.08340118839663793 0.7108865718356642 chr2 243199373 11042181 0.04540382182646499 0.3641203827458122 chr3 198022430 11002776 0.05556328139191101 0.2742266739906204 chr4 191154276 7519193 0.03933573005711889 0.23353825683622548 chr5 180915260 8668495 0.047914670105772175 0.25382532037277383 chr6 171115067 12958980 0.07573254785331089 0.41754528757563664 chr7 159138663 10778290 0.06772892141239116 0.9347612368172565 chr8 146364022 20948072 0.14312309619368072 0.6258614095511894 chr9 141213431 5448866 0.038586032230886025 0.30291840096290923 chr10 135534747 8099620 0.059760468656793964 0.31694599388603184 chr11 135006516 7535040 0.05581241723177272 0.2932574126075036 chr12 133851895 5602729 0.04185767411062802 0.2412770349936508 chr13 115169878 5553522 0.048220264677192766 0.256124655325147 chr14 107349540 3636560 0.033875878741539085 0.22618464935534274 chr15 102531392 2933142 0.028607258155629058 0.19613940880429076 chr16 90354753 3929896 0.04349407053329004 0.25297072572592133 chr17 81195210 2663700 0.03280612243012858 0.21220373192033254 chr18 78077248 5739997 0.07351689700948476 0.4864210660950088 chr19 59128983 2651541 0.044843338502879374 0.4453683272769627 chr20 63025520 3788819 0.060115632524729665 0.2892835764936869 chr21 48129895 2503743 0.0520205373396306 0.2729338161573565 chr22 51304566 1614826 0.031475288183901606 0.2037176239869626 chrMT 16571 81188 4.89940257075614 3.806819769494806 chrX 155270560 12818085 0.08255322193724296 0.35943451182514013 chrY 59373566 337822 0.005689771101166469 0.1007109177990116