BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013343.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,223,827 number of mapped reads = 2,011,855 (90.47%) number of supplementary alignments = 11,639 (0.52%) number of secondary alignments = 0 number of mapped bases = 133,985,329 bp number of sequenced bases = 133,920,907 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,188 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7285 >>>>>>> ACTG content number of A's = 36,271,308 bp (27.08%) number of C's = 25,835,794 bp (19.29%) number of T's = 41,131,244 bp (30.71%) number of G's = 30,650,263 bp (22.89%) number of N's = 32,298 bp (0.02%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,072,500 number of insertions = 8,980 mapped reads with insertion percentage = 0.44% number of deletions = 36,464 mapped reads with deletion percentage = 1.79% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.3601X There is a 3.62% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9994303 0.04009740461188259 0.5610773291137615 chr2 243199373 13101769 0.0538725443177849 0.43559874564585327 chr3 198022430 8191676 0.04136741479235458 0.23414874088547163 chr4 191154276 8027306 0.04199386049831289 0.24556108713705627 chr5 180915260 7216006 0.03988611021535718 0.23195102166411002 chr6 171115067 7047707 0.041186945857900406 0.28810345387818737 chr7 159138663 8094402 0.05086383062046965 0.6078841980351217 chr8 146364022 7294013 0.049834740124864836 0.33353788185417527 chr9 141213431 4830499 0.03420707907026209 0.30177721268094243 chr10 135534747 6432896 0.04746307601843238 0.3766231924987041 chr11 135006516 5647333 0.04183007729789872 0.2804891732447643 chr12 133851895 6630685 0.04953747573017177 0.2609270923951355 chr13 115169878 3439791 0.029867106397386302 0.2011089618511795 chr14 107349540 4432654 0.04129178383065265 0.25129954729381504 chr15 102531392 3873831 0.03778190195642716 0.22486410214022765 chr16 90354753 4629097 0.051232468091634314 0.298666048609422 chr17 81195210 3761383 0.04632518346833514 0.2721616063059183 chr18 78077248 3256388 0.04170725894437263 0.543159736574199 chr19 59128983 2921482 0.049408629267308726 0.465659135479915 chr20 63025520 3238093 0.05137748962642434 0.2692081826773164 chr21 48129895 2291865 0.0476183253672172 0.2682116995955526 chr22 51304566 1479175 0.02883125451251259 0.19503276851144527 chrMT 16571 421073 25.410234747450364 14.838224729269433 chrX 155270560 7420257 0.047789207432497184 0.27484095509842804 chrY 59373566 311645 0.005248884663589181 0.12437670931355455