BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818856.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,867,052 number of mapped reads = 1,792,438 (96%) number of supplementary alignments = 27,393 (1.47%) number of secondary alignments = 0 number of mapped bases = 166,051,376 bp number of sequenced bases = 165,946,157 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 414,166 duplication rate = 19.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4164 >>>>>>> ACTG content number of A's = 47,798,416 bp (28.8%) number of C's = 35,204,484 bp (21.21%) number of T's = 47,353,006 bp (28.54%) number of G's = 35,587,897 bp (21.45%) number of N's = 2,354 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,007,250 number of insertions = 24,880 mapped reads with insertion percentage = 1.35% number of deletions = 53,737 mapped reads with deletion percentage = 2.92% homopolymer indels = 39.6% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.6037X There is a 3.65% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 15787477 0.06333976997393319 0.9199371167033639 chr2 243199373 14453378 0.059430161442069175 0.8967013035862278 chr3 198022430 9906475 0.05002703481620744 0.30528344543996033 chr4 191154276 7609670 0.03980904931470118 0.3731943635587235 chr5 180915260 7824187 0.043247800102655796 0.300244912581539 chr6 171115067 7172154 0.0419142167065861 0.30477726752403694 chr7 159138663 13327999 0.0837508544356691 1.1632653054876687 chr8 146364022 16841798 0.11506788191431361 0.5830279236582817 chr9 141213431 5852410 0.04144372074636442 0.47077080003980964 chr10 135534747 7563602 0.05580563041889177 0.7991997182189233 chr11 135006516 7191474 0.05326760672795971 0.37936491938945793 chr12 133851895 6206566 0.04636890646934808 0.2932282195179449 chr13 115169878 4103923 0.035633648930321865 0.2556184316197751 chr14 107349540 5600642 0.052172016759457006 0.3400434524854556 chr15 102531392 4105295 0.040039395934466586 0.27265460291148813 chr16 90354753 4189457 0.04636675837075223 0.682609593857731 chr17 81195210 5183569 0.06384082262980784 0.43545581479499257 chr18 78077248 2734119 0.0350181271757939 0.5445936667249905 chr19 59128983 2617492 0.04426749568819745 0.8171276479215268 chr20 63025520 6856875 0.10879521501766269 0.48510796755139174 chr21 48129895 2003510 0.041627142548306 0.32055806840070705 chr22 51304566 1909016 0.037209475663433154 0.2961740103112905 chrMT 16571 276882 16.708828676603705 10.536344672028475 chrX 155270560 6168711 0.03972878696386488 0.3141888949583849 chrY 59373566 564695 0.009510882334404506 0.771681879050102