BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708562.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,494,671 number of mapped reads = 3,703,583 (82.4%) number of supplementary alignments = 81 (0%) number of secondary alignments = 0 number of mapped bases = 184,700,359 bp number of sequenced bases = 184,682,798 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,249 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3356 >>>>>>> ACTG content number of A's = 57,312,343 bp (31.03%) number of C's = 34,965,830 bp (18.93%) number of T's = 57,074,072 bp (30.9%) number of G's = 35,323,906 bp (19.13%) number of N's = 6,647 bp (0%) GC percentage = 38.06% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 293,561 number of insertions = 12,227 mapped reads with insertion percentage = 0.33% number of deletions = 10,076 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 0.0597X std coverageData = 0.2526X There is a 5.61% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.02% 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 13854646 0.055585201530952255 0.24534986850593243 chr2 243199373 17484785 0.07189486051841096 0.2763063372423375 chr3 198022430 14970617 0.07560061251647099 0.28327645474528373 chr4 191154276 14790631 0.07737536041307284 0.28605926136940185 chr5 180915260 14237842 0.07869895552204938 0.2885908272420638 chr6 171115067 11010837 0.06434755976222713 0.26118491001807614 chr7 159138663 10081250 0.06334884188388588 0.2601929198250942 chr8 146364022 9092036 0.06211933695016935 0.2563374685205594 chr9 141213431 8103946 0.057387926506792405 0.24843578777916767 chr10 135534747 8572980 0.06325300478112819 0.2584104973977159 chr11 135006516 7724316 0.05721439400747146 0.2472298257386499 chr12 133851895 8977717 0.0670720201607904 0.2674542039981263 chr13 115169878 6444217 0.05595401429530037 0.2444460569113761 chr14 107349540 5274646 0.04913524547939376 0.2294900896481436 chr15 102531392 4282880 0.04177140206971929 0.211787158520165 chr16 90354753 3084118 0.03413343402089761 0.19094555611542804 chr17 81195210 3355984 0.04133229041466855 0.20978602152279305 chr18 78077248 6190194 0.07928294296438317 0.2905058900234058 chr19 59128983 1088887 0.018415452875284528 0.13815354765545643 chr20 63025520 2661184 0.04222391183761753 0.21183548447451186 chr21 48129895 2389154 0.0496397093739764 0.23175405009509215 chr22 51304566 1048217 0.020431261420279824 0.14787312958128465 chrMT 16571 300 0.018103916480598635 0.13332728411192565 chrX 155270560 9742709 0.06274665976602391 0.25866953298671613 chrY 59373566 236266 0.003979312948796102 0.06558927437961276