BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714168.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 49,940 number of mapped reads = 3,473 (6.95%) number of supplementary alignments = 95 (0.19%) number of secondary alignments = 0 number of mapped bases = 325,744 bp number of sequenced bases = 321,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,582 duplication rate = 37.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 16.6156 >>>>>>> ACTG content number of A's = 59,443 bp (18.52%) number of C's = 38,772 bp (12.08%) number of T's = 51,343 bp (15.99%) number of G's = 171,490 bp (53.41%) number of N's = 5 bp (0%) GC percentage = 65.49% >>>>>>> Mismatches and indels general error rate = 0.0365 number of mismatches = 10,219 number of insertions = 314 mapped reads with insertion percentage = 7.31% number of deletions = 698 mapped reads with deletion percentage = 19.49% homopolymer indels = 36.96% >>>>>>> Coverage mean coverageData = 0.0001X std coverageData = 0.1547X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 6092 2.444126307713392E-5 0.014680102552337489 chr2 243199373 156764 6.445904776242988E-4 0.5424035568337359 chr3 198022430 15377 7.765281943060693E-5 0.036541794117179185 chr4 191154276 6274 3.282165657649217E-5 0.014665488273862475 chr5 180915260 7094 3.9211728186997606E-5 0.02461135077342805 chr6 171115067 16876 9.862369396144409E-5 0.039945939648869624 chr7 159138663 5002 3.143170808215223E-5 0.023883859241211673 chr8 146364022 5716 3.9053313252077754E-5 0.017192937502475823 chr9 141213431 2306 1.6329891453455303E-5 0.005593997296578057 chr10 135534747 8068 5.9527170549113875E-5 0.03465388210930221 chr11 135006516 5774 4.276830608679658E-5 0.028207770988145163 chr12 133851895 14931 1.1154866354338876E-4 0.04320005578216031 chr13 115169878 11279 9.793359336544578E-5 0.05745570072886801 chr14 107349540 6682 6.224525973748933E-5 0.034675710759887006 chr15 102531392 8088 7.888315804782988E-5 0.033415392353342885 chr16 90354753 2998 3.318032422710513E-5 0.014963833116449065 chr17 81195210 1354 1.6675860558769415E-5 0.011731623704601362 chr18 78077248 5782 7.405486422882118E-5 0.0294323787056126 chr19 59128983 651 1.1009829139121165E-5 0.004581255860323431 chr20 63025520 5451 8.648877470586518E-5 0.026171004279400396 chr21 48129895 2642 5.489311788442505E-5 0.02742192711990507 chr22 51304566 1647 3.210240585604018E-5 0.0117679945692693 chrMT 16571 931 0.05618248747812443 0.32616833759456965 chrX 155270560 27596 1.7772847602275666E-4 0.048556338014099504 chrY 59373566 369 6.214886941437878E-6 0.003202663142660849