BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013318.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 = 1,542,484 number of mapped reads = 1,111,877 (72.08%) number of supplementary alignments = 11,888 (0.77%) number of secondary alignments = 0 number of mapped bases = 71,539,781 bp number of sequenced bases = 71,503,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,635 duplication rate = 11.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4853 >>>>>>> ACTG content number of A's = 19,554,035 bp (27.35%) number of C's = 12,786,490 bp (17.88%) number of T's = 23,221,960 bp (32.48%) number of G's = 15,932,993 bp (22.28%) number of N's = 8,260 bp (0.01%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 568,784 number of insertions = 5,273 mapped reads with insertion percentage = 0.47% number of deletions = 20,519 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.3012X There is a 1.18% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 5325442 0.021365812364415333 0.3632309510977285 chr2 243199373 5814404 0.023907972821952957 0.3622201870695416 chr3 198022430 4760312 0.024039256563006525 0.272670017330491 chr4 191154276 4560018 0.023855171306761666 0.26793919412526535 chr5 180915260 5261561 0.029083013782253635 0.30570133792319204 chr6 171115067 4152019 0.024264485137360816 0.28836816431893514 chr7 159138663 4059842 0.02551134918105979 0.32257373932995137 chr8 146364022 3932666 0.02686907578967733 0.3796276012183464 chr9 141213431 2719515 0.019258189399845402 0.2556869419286912 chr10 135534747 3725022 0.0274838894265247 0.3313111553313251 chr11 135006516 3317009 0.02456925116118099 0.29716552727681295 chr12 133851895 3048008 0.02277149680996298 0.26393432767737185 chr13 115169878 2121151 0.018417584848010347 0.24150873901704262 chr14 107349540 2298290 0.021409407064063805 0.2597552584457407 chr15 102531392 2034458 0.019842293763065268 0.24810634773717147 chr16 90354753 1820341 0.020146599260804796 0.24354414835592567 chr17 81195210 1937356 0.023860471572153086 0.28129134923117016 chr18 78077248 2226302 0.028514094144301807 0.4135808673082378 chr19 59128983 1237031 0.020920890859901987 0.29942284466646096 chr20 63025520 1605265 0.025470079421796122 0.2869162742453293 chr21 48129895 1000258 0.020782467944299485 0.24919483017700908 chr22 51304566 713033 0.013898041745446205 0.21189533017234147 chrMT 16571 66644 4.021724699776718 5.685450181230469 chrX 155270560 3610676 0.023254092726914876 0.26624984119783884 chrY 59373566 193158 0.003253265939930238 0.08676543566542896