BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008688.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 = 880,013 number of mapped reads = 745,104 (84.67%) number of supplementary alignments = 4,387 (0.5%) number of secondary alignments = 0 number of mapped bases = 48,710,967 bp number of sequenced bases = 48,669,641 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,839 duplication rate = 1.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5333 >>>>>>> ACTG content number of A's = 13,488,848 bp (27.72%) number of C's = 8,995,838 bp (18.48%) number of T's = 15,060,595 bp (30.94%) number of G's = 11,112,050 bp (22.83%) number of N's = 12,310 bp (0.03%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 476,824 number of insertions = 3,918 mapped reads with insertion percentage = 0.52% number of deletions = 23,376 mapped reads with deletion percentage = 3.08% homopolymer indels = 42.47% >>>>>>> Coverage mean coverageData = 0.0157X std coverageData = 0.237X There is a 1.46% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 4272486 0.01714132539713913 0.5105125699209665 chr2 243199373 4082270 0.01678569294666726 0.22913795274683127 chr3 198022430 4059461 0.02050000598417058 0.15487031505148588 chr4 191154276 3323873 0.017388431321306148 0.14762966868227395 chr5 180915260 2838734 0.01569095940276127 0.1314881725662408 chr6 171115067 2587915 0.015123828926181 0.14212042922368623 chr7 159138663 2297479 0.014436963065348866 0.20941476783574273 chr8 146364022 2882854 0.019696466116515984 0.32735138284611487 chr9 141213431 1925351 0.013634333408413538 0.19878266427224572 chr10 135534747 3564436 0.026299056728235157 0.3424257837321903 chr11 135006516 1949063 0.01443680688715795 0.1580600524696685 chr12 133851895 2098169 0.01567530291595797 0.1326592174720699 chr13 115169878 1005242 0.008728341276874496 0.09657435205657071 chr14 107349540 1486249 0.013844949871233728 0.13059392639270434 chr15 102531392 1104235 0.010769726017179206 0.10765459550240514 chr16 90354753 1356581 0.015013941767955473 0.15502539510239313 chr17 81195210 1348576 0.01660905858855467 0.14834542872414197 chr18 78077248 954352 0.012223176718523686 0.34602735416653924 chr19 59128983 968942 0.016386921452716342 0.3383711019097229 chr20 63025520 1040521 0.016509518683860126 0.13705829502923064 chr21 48129895 511125 0.010619699045676289 0.11927285174543621 chr22 51304566 619255 0.012070173247348005 0.11437984752452432 chrMT 16571 79590 4.802969042302818 3.3153560482354156 chrX 155270560 2196397 0.014145611376683385 0.13585675730849434 chrY 59373566 157811 0.0026579336669790054 0.10291113648227955