BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013245.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 = 1,410,290 number of mapped reads = 1,085,417 (76.96%) number of supplementary alignments = 15,501 (1.1%) number of secondary alignments = 0 number of mapped bases = 68,278,927 bp number of sequenced bases = 68,204,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,197 duplication rate = 10.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1753 >>>>>>> ACTG content number of A's = 19,462,389 bp (28.54%) number of C's = 11,595,629 bp (17%) number of T's = 22,795,596 bp (33.42%) number of G's = 14,336,927 bp (21.02%) number of N's = 14,455 bp (0.02%) GC percentage = 38.02% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 724,560 number of insertions = 5,702 mapped reads with insertion percentage = 0.52% number of deletions = 41,658 mapped reads with deletion percentage = 3.75% homopolymer indels = 41.35% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.3034X There is a 1.24% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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% 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 4642717 0.018626701836782986 0.39458930039446966 chr2 243199373 4860676 0.019986383764237746 0.3466727578930566 chr3 198022430 4353988 0.021987347594916395 0.23885322333008108 chr4 191154276 6907170 0.036134007276928504 0.33717995163143816 chr5 180915260 1310946 0.007246188077224663 0.13219016895925711 chr6 171115067 4149402 0.024249191335091493 0.25948714109485116 chr7 159138663 6379491 0.04008762471505746 0.4209983894012091 chr8 146364022 1190381 0.008133016459468434 0.3178820718437674 chr9 141213431 2984600 0.021135383361657715 0.2681226816811328 chr10 135534747 4435406 0.032725231707556146 0.4367124588400002 chr11 135006516 3856949 0.02856861368083893 0.301869838494741 chr12 133851895 5829797 0.0435540864027364 0.3473370899864612 chr13 115169878 313605 0.002722977617463483 0.07739411253832958 chr14 107349540 2337105 0.021770982903140525 0.24526531907234958 chr15 102531392 750532 0.0073200215598360355 0.1320495264071357 chr16 90354753 1649558 0.018256460730959 0.23175320336978877 chr17 81195210 1212937 0.014938529009285153 0.2077180510100565 chr18 78077248 1394323 0.01785824981946085 0.3410340045688688 chr19 59128983 327132 0.005532515247218103 0.3355162188438052 chr20 63025520 707772 0.011229927178704753 0.1676939897891662 chr21 48129895 1123190 0.023336639317413845 0.2722174849133844 chr22 51304566 116785 0.0022763081165134503 0.0632144779524858 chrMT 16571 9840 0.5938084605636352 1.1023021303646068 chrX 155270560 7194577 0.04633574452233572 0.369990911957779 chrY 59373566 240048 0.004043011329317832 0.15948848820193678