BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230403.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 = 1,424,021 number of mapped reads = 768,143 (53.94%) number of supplementary alignments = 9,927 (0.7%) number of secondary alignments = 0 number of mapped bases = 49,329,743 bp number of sequenced bases = 49,310,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,363 duplication rate = 12.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1448 >>>>>>> ACTG content number of A's = 13,501,887 bp (27.38%) number of C's = 9,341,811 bp (18.95%) number of T's = 15,300,543 bp (31.03%) number of G's = 11,156,459 bp (22.63%) number of N's = 9,300 bp (0.02%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 442,187 number of insertions = 3,987 mapped reads with insertion percentage = 0.51% number of deletions = 12,358 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 0.375X There is a 0.61% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 2795665 0.011216280981703151 0.3823098515050743 chr2 243199373 10582628 0.04351420757980326 0.6182809276531112 chr3 198022430 2298230 0.011605907472198983 0.25815188595086064 chr4 191154276 2155834 0.011277979468269911 0.27694439053706854 chr5 180915260 1978446 0.01093576075340466 0.2615258912643109 chr6 171115067 3341322 0.01952675505775304 0.38687806287806836 chr7 159138663 2147440 0.013494143783274088 0.2900172856200496 chr8 146364022 1929609 0.01318362923915824 0.30162132539102454 chr9 141213431 1998019 0.01414893035209944 0.2866909215669142 chr10 135534747 1562151 0.011525834035754684 0.26203891552581 chr11 135006516 2718303 0.020134605947464048 0.353186847008526 chr12 133851895 1667812 0.012460129907014018 0.27392805416644966 chr13 115169878 1583864 0.013752415366802767 0.3335690177273767 chr14 107349540 1416797 0.01319797923679971 0.5566599157350293 chr15 102531392 942691 0.009194169528099257 0.7047934654582403 chr16 90354753 1767654 0.019563486604849665 0.35224162642988 chr17 81195210 1965909 0.0242121302475848 0.39162490242339576 chr18 78077248 908882 0.011640804757872613 0.32120252942088107 chr19 59128983 810213 0.013702468043463558 0.27992825209503747 chr20 63025520 800451 0.012700426747768206 0.26518642371158346 chr21 48129895 725440 0.01507254482894675 0.28028197747093936 chr22 51304566 351022 0.006841925141711559 0.1832286242066459 chrMT 16571 8019 0.4839176875264015 1.4165684266138825 chrX 155270560 2754181 0.017737947232237716 0.37011906834293934 chrY 59373566 119161 0.0020069705767714876 0.10664857948407903