BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124777.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 654,711 number of mapped reads = 654,094 (99.91%) number of supplementary alignments = 289,232 (44.18%) number of secondary alignments = 0 number of mapped bases = 98,235,824 bp number of sequenced bases = 98,173,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 940,753 duplication rate = 30.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2625 >>>>>>> ACTG content number of A's = 27,524,643 bp (28.04%) number of C's = 18,176,262 bp (18.51%) number of T's = 31,913,200 bp (32.51%) number of G's = 20,559,843 bp (20.94%) number of N's = 1 bp (0%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 728,465 number of insertions = 13,908 mapped reads with insertion percentage = 2.11% number of deletions = 53,842 mapped reads with deletion percentage = 7.99% homopolymer indels = 78.31% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 57.638X There is a 0.01% 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 143215 5.745823196966078E-4 0.46374469067624663 chr2 243199373 18259 7.507831856129005E-5 0.018947518497686614 chr3 198022430 12996 6.56289290056687E-5 0.008157123290813745 chr4 191154276 10654 5.573508593655524E-5 0.008442416847722928 chr5 180915260 14954 8.265748284583622E-5 0.011201666514680072 chr6 171115067 13838 8.086955896174824E-5 0.022175179588324403 chr7 159138663 16232 1.0199909747890743E-4 0.03741558459068835 chr8 146364022 85587214 0.584755822028449 258.58554581233426 chr9 141213431 9556 6.767061696843837E-5 0.008222062573791962 chr10 135534747 12311460 0.09083618977796151 60.579158630978164 chr11 135006516 11995 8.88475634761214E-5 0.024188629462415616 chr12 133851895 12937 9.66516013837533E-5 0.02291198272663674 chr13 115169878 6680 5.800127703530258E-5 0.008899515705186628 chr14 107349540 5478 5.102956193384713E-5 0.007994962356078083 chr15 102531392 6570 6.407793624805172E-5 0.010774828160425682 chr16 90354753 5254 5.814857354543374E-5 0.007623848102517693 chr17 81195210 14760 1.817841224870285E-4 0.08776614794688171 chr18 78077248 4694 6.0119946850585714E-5 0.00865057968564275 chr19 59128983 3100 5.2427757805338884E-5 0.008347181121282837 chr20 63025520 6426 1.0195869863509258E-4 0.01076545575967926 chr21 48129895 5125 1.0648267568420833E-4 0.033355700709818616 chr22 51304566 1560 3.0406650355447894E-5 0.005512371135352324 chrMT 16571 151 0.00911230462856798 0.0950224738307952 chrX 155270560 11478 7.392257746735762E-5 0.015132574313533306 chrY 59373566 1238 2.0851029901084264E-5 0.0045477661592199965