BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708638.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 = 3,718,811 number of mapped reads = 3,427,646 (92.17%) number of supplementary alignments = 70 (0%) number of secondary alignments = 0 number of mapped bases = 171,043,330 bp number of sequenced bases = 171,026,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,343 duplication rate = 0.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8811 >>>>>>> ACTG content number of A's = 53,083,071 bp (31.04%) number of C's = 32,340,156 bp (18.91%) number of T's = 53,083,814 bp (31.04%) number of G's = 32,514,493 bp (19.01%) number of N's = 5,354 bp (0%) GC percentage = 37.92% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 267,391 number of insertions = 11,437 mapped reads with insertion percentage = 0.33% number of deletions = 9,605 mapped reads with deletion percentage = 0.28% homopolymer indels = 48.79% >>>>>>> Coverage mean coverageData = 0.0553X std coverageData = 0.2417X There is a 5.24% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.01% 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 13684602 0.054902980562684334 0.24246136438373136 chr2 243199373 14664464 0.06029811598239606 0.2512076585431068 chr3 198022430 13468639 0.06801572427931522 0.2670857475464353 chr4 191154276 14503743 0.07587454125274185 0.2817499088287932 chr5 180915260 11900795 0.06578104577800678 0.26243771117717996 chr6 171115067 11280502 0.06592348761433148 0.2626710507900562 chr7 159138663 9659147 0.06069641919764024 0.2532995264595872 chr8 146364022 10016502 0.06843554763751983 0.267992015076439 chr9 141213431 6845293 0.04847480123898413 0.22647987315539497 chr10 135534747 7191960 0.05306358818820092 0.23578707326215612 chr11 135006516 7753865 0.05743326492478333 0.24634068549350616 chr12 133851895 7812029 0.058363230494420715 0.24815416201998317 chr13 115169878 6428858 0.05582065477224869 0.24259551759461798 chr14 107349540 5586031 0.05203590998154254 0.2352058202788346 chr15 102531392 4426436 0.04317151960640503 0.21332200989079098 chr16 90354753 2935328 0.032486702719446314 0.18468298954113532 chr17 81195210 2580653 0.03178331578919495 0.18318640405429992 chr18 78077248 7025259 0.0899783122478907 0.3092478632301318 chr19 59128983 1330637 0.0225039723751041 0.1528517354529444 chr20 63025520 2584567 0.04100826141537587 0.2076628852220557 chr21 48129895 2013332 0.04183121529768557 0.21189675356083612 chr22 51304566 860711 0.016776498996210202 0.13243621839833236 chrMT 16571 450 0.027155874720897956 0.1801473619454558 chrX 155270560 5595414 0.03603654163416426 0.1933251423889493 chrY 59373566 894113 0.015059108964416926 0.12625867990453188