BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080671.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,474,474 number of mapped reads = 1,326,278 (89.95%) number of supplementary alignments = 11,705 (0.79%) number of secondary alignments = 0 number of mapped bases = 87,258,811 bp number of sequenced bases = 87,226,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,611 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2249 >>>>>>> ACTG content number of A's = 23,251,041 bp (26.66%) number of C's = 16,193,300 bp (18.56%) number of T's = 27,514,008 bp (31.54%) number of G's = 20,264,130 bp (23.23%) number of N's = 4,020 bp (0%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 596,535 number of insertions = 6,306 mapped reads with insertion percentage = 0.47% number of deletions = 20,092 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.58% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.234X There is a 2.43% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 10644777 0.042707123285361845 0.2620777614288921 chr2 243199373 5913114 0.024313853802575388 0.3608825744550946 chr3 198022430 5388046 0.027209271192157373 0.18591200462716387 chr4 191154276 3663639 0.019165875211705964 0.1593689950870362 chr5 180915260 3957030 0.021872284294868215 0.16617370812223983 chr6 171115067 5054367 0.02953782556155619 0.22742244244319454 chr7 159138663 5542986 0.03483117110265027 0.42268886590302857 chr8 146364022 10455650 0.0714359297942769 0.32645006171729224 chr9 141213431 2756683 0.019521393825492422 0.17194363459165798 chr10 135534747 4148869 0.030611109636704454 0.20579225668748388 chr11 135006516 3629581 0.026884487560585594 0.19325930152846463 chr12 133851895 2854161 0.021323276745540284 0.16526148217477915 chr13 115169878 1838516 0.015963514348777897 0.1428113501687218 chr14 107349540 1748343 0.016286450784977747 0.14362621775271003 chr15 102531392 1760498 0.01717033159951637 0.15681714598506666 chr16 90354753 2052879 0.02272021041328064 0.17159032354353812 chr17 81195210 1477693 0.01819926323240004 0.15385879165638017 chr18 78077248 2718474 0.0348177486993394 0.24247837655757978 chr19 59128983 1531299 0.02589760422566375 0.19809769642583827 chr20 63025520 2360375 0.037451099173794994 0.2215717426342141 chr21 48129895 1243168 0.0258294351151192 0.18148623720873672 chr22 51304566 876914 0.017092318839613613 0.14612590127723965 chrMT 16571 15663 0.9452054794520548 1.1726327997378758 chrX 155270560 5456117 0.03513941728554338 0.21919711295037414 chrY 59373566 169969 0.0028627049283177636 0.060623342549976034