BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818883.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 = 1,818,296 number of mapped reads = 1,795,078 (98.72%) number of supplementary alignments = 27,277 (1.5%) number of secondary alignments = 0 number of mapped bases = 166,285,588 bp number of sequenced bases = 166,179,495 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 345,045 duplication rate = 16.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2341 >>>>>>> ACTG content number of A's = 47,188,813 bp (28.4%) number of C's = 35,066,724 bp (21.1%) number of T's = 47,909,384 bp (28.83%) number of G's = 36,012,189 bp (21.67%) number of N's = 2,385 bp (0%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,034,303 number of insertions = 24,596 mapped reads with insertion percentage = 1.33% number of deletions = 53,783 mapped reads with deletion percentage = 2.92% homopolymer indels = 39.64% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.6581X There is a 3.84% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 14374163 0.05766951730082149 0.9470367751655936 chr2 243199373 12566647 0.051672201473973375 0.9642535589426866 chr3 198022430 10565839 0.053356778825509814 0.30108822037098204 chr4 191154276 8372425 0.04379930794747171 0.38822470881375143 chr5 180915260 7306118 0.04038419976291663 0.2787730026367651 chr6 171115067 8201435 0.04792935621501992 0.3241902726506284 chr7 159138663 13664001 0.08586223323995125 1.4769342315656475 chr8 146364022 16527542 0.11292079688818608 0.5967822659609263 chr9 141213431 6055256 0.04288017051295921 0.5424882713782838 chr10 135534747 7744337 0.057139126101736847 0.8561214251515304 chr11 135006516 7209737 0.05340288168017016 0.3923014788260259 chr12 133851895 6390149 0.0477404447654626 0.28475416445159507 chr13 115169878 5255112 0.04562922259933279 0.2755878622695316 chr14 107349540 5164886 0.04811279116799196 0.3145223602990874 chr15 102531392 4614775 0.045008410692405305 0.27419675903566226 chr16 90354753 4219755 0.04670208107369847 0.6962684957768104 chr17 81195210 4290252 0.05283873272819911 0.41675772386819787 chr18 78077248 3144688 0.04027662450397842 0.6253054750608514 chr19 59128983 2913711 0.049277204717016694 0.8308932790070147 chr20 63025520 6834701 0.10844338928104044 0.46959061557868725 chr21 48129895 1623366 0.033728849813613765 0.29835250451982825 chr22 51304566 1507438 0.029382141152894656 0.2535350834327266 chrMT 16571 285966 17.25701526763623 10.648949703014276 chrX 155270560 6805502 0.043829957205023286 0.3445283259590329 chrY 59373566 647787 0.010910360344534468 0.779833588541254