BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819085.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,018,259 number of mapped reads = 902,887 (88.67%) number of supplementary alignments = 5,127 (0.5%) number of secondary alignments = 0 number of mapped bases = 50,935,804 bp number of sequenced bases = 50,916,572 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,124 duplication rate = 6.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1115 >>>>>>> ACTG content number of A's = 12,227,067 bp (24.01%) number of C's = 9,414,473 bp (18.49%) number of T's = 16,532,877 bp (32.47%) number of G's = 12,741,527 bp (25.02%) number of N's = 628 bp (0%) GC percentage = 43.51% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 285,872 number of insertions = 3,456 mapped reads with insertion percentage = 0.38% number of deletions = 11,394 mapped reads with deletion percentage = 1.25% homopolymer indels = 42.73% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 0.191X There is a 1.33% of reference with a coverageData >= 1X There is a 0.22% 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 0.01% 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 4872036 0.01954673565286724 0.27947735868776064 chr2 243199373 4014538 0.01650718893917543 0.23399342798515188 chr3 198022430 2688503 0.01357675996603011 0.1404725501207146 chr4 191154276 2989064 0.01563691936454511 0.17829410796447834 chr5 180915260 2733757 0.015110704315379477 0.14729495403392937 chr6 171115067 2575891 0.015053560420836583 0.1579666463205163 chr7 159138663 2605893 0.016374983620416617 0.2121154265399456 chr8 146364022 4563867 0.031181617843215596 0.24019781938888948 chr9 141213431 2101698 0.014883131052881223 0.16288080367893143 chr10 135534747 2691431 0.01985786714900497 0.22800106058340858 chr11 135006516 1716068 0.012711001297152205 0.17060530273128016 chr12 133851895 2345521 0.017523255834368277 0.1593794789549096 chr13 115169878 1099476 0.009546558693063823 0.11622313378585608 chr14 107349540 1192247 0.011106214334965944 0.12769696570497063 chr15 102531392 1323345 0.012906730067607002 0.13834955562333057 chr16 90354753 1643546 0.018189923002722392 0.16911918460580053 chr17 81195210 1791071 0.022058825883940692 0.1849180226825827 chr18 78077248 1169317 0.014976411566145363 0.24453455805512492 chr19 59128983 1050019 0.0177581102654852 0.21505867373250798 chr20 63025520 1414077 0.02243657807186676 0.18320173282991056 chr21 48129895 718450 0.014927312847867214 0.16827760191096341 chr22 51304566 407724 0.007947128916361948 0.10561786041339427 chrMT 16571 39769 2.3999155150564238 2.350177322198577 chrX 155270560 2971057 0.01913470911678299 0.17404682454410483 chrY 59373566 217439 0.003662218974686479 0.14565041772823298