BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549049.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 3,741,160 number of mapped reads = 3,050,414 (81.54%) number of secondary alignments = 0 number of mapped bases = 120,531,155 bp number of sequenced bases = 120,520,424 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,176 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.0586 >>>>>>> ACTG content number of A's = 33,375,012 bp (27.69%) number of C's = 26,322,874 bp (21.84%) number of T's = 34,275,998 bp (28.44%) number of G's = 26,545,519 bp (22.03%) number of N's = 1,021 bp (0%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 355,548 number of insertions = 4,035 mapped reads with insertion percentage = 0.13% number of deletions = 8,284 mapped reads with deletion percentage = 0.27% homopolymer indels = 38.53% >>>>>>> Coverage mean coverageData = 0.0389X std coverageData = 0.3451X There is a 3.42% of reference with a coverageData >= 1X There is a 0.34% 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 9775967 0.03922143487859154 0.5028809589209202 chr2 243199373 10380201 0.04268185757205879 0.37758655452496787 chr3 198022430 7982936 0.04031329178214811 0.22378315661921094 chr4 191154276 7773945 0.0406684337001177 0.24256279686882914 chr5 180915260 7685886 0.04248334828139981 0.23156878531884928 chr6 171115067 6936472 0.04053688621119495 0.23541091980257361 chr7 159138663 6703682 0.042124785225825356 0.4181316272009477 chr8 146364022 6090841 0.041614331970188684 0.6489351435072744 chr9 141213431 5137404 0.03638042049980359 0.3692490757742065 chr10 135534747 5850795 0.043168229029859034 0.30685902679827787 chr11 135006516 5501780 0.04075195896470656 0.2753066883365997 chr12 133851895 5676608 0.042409619975869596 0.23428049506407958 chr13 115169878 3761498 0.032660432270319846 0.20015357433914055 chr14 107349540 3709532 0.0345556394559306 0.24076268047544813 chr15 102531392 3402433 0.03318430515407418 0.20309464718296238 chr16 90354753 3634119 0.0402205626083666 0.24488149682739035 chr17 81195210 3322636 0.04092157653142347 0.23413038418314752 chr18 78077248 3302346 0.04229588112531835 0.6011513554756128 chr19 59128983 2779930 0.04701467637283733 0.5449634109170143 chr20 63025520 2545109 0.040382197560607194 0.23061387207822048 chr21 48129895 1545840 0.03211808378140031 0.24595507588731647 chr22 51304566 1414534 0.02757130817557252 0.26598614134197923 chrMT 16571 9809 0.5919377225273067 0.9588374129272935 chrX 155270560 4562572 0.029384656048126574 0.2322106009865374 chrY 59373566 1044280 0.01758829846938956 0.20382268392857036