BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238286.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 = 1,490,773 number of mapped reads = 1,164,689 (78.13%) number of supplementary alignments = 12,011 (0.81%) number of secondary alignments = 0 number of mapped bases = 75,362,305 bp number of sequenced bases = 75,311,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 144,681 duplication rate = 9.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2116 >>>>>>> ACTG content number of A's = 20,540,223 bp (27.27%) number of C's = 14,439,436 bp (19.17%) number of T's = 23,198,591 bp (30.8%) number of G's = 17,119,276 bp (22.73%) number of N's = 14,447 bp (0.02%) GC percentage = 41.9% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 777,234 number of insertions = 6,098 mapped reads with insertion percentage = 0.52% number of deletions = 30,705 mapped reads with deletion percentage = 2.6% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2908X There is a 1.38% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% 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% 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 5587959 0.022419037423381184 0.37014633085065735 chr2 243199373 6422379 0.02640787647096442 0.3450873861552064 chr3 198022430 4972038 0.02510845867309072 0.251245364129314 chr4 191154276 4674342 0.024453243201318708 0.2554543458139404 chr5 180915260 4843341 0.026771323767823676 0.25916637418393434 chr6 171115067 4395844 0.025689403493615207 0.27875783361747186 chr7 159138663 4765308 0.02994437624501093 0.3889976335665578 chr8 146364022 3767468 0.025740396775923526 0.3144504738676324 chr9 141213431 2899974 0.02053610608752931 0.25964798356157787 chr10 135534747 3306180 0.02439359701612163 0.28125714452058775 chr11 135006516 3152627 0.023351665485538492 0.26431297732120557 chr12 133851895 3441861 0.025713950482359627 0.2560092922176878 chr13 115169878 2780308 0.024140930322076055 0.251713614627793 chr14 107349540 2679843 0.024963712001001587 0.27089188782718526 chr15 102531392 2212679 0.021580502876621437 0.2714606497524219 chr16 90354753 2204918 0.024402899978045428 0.25159685015948646 chr17 81195210 2030911 0.025012694714380317 0.2585694155062262 chr18 78077248 2019530 0.02586579383535649 0.38110120311427803 chr19 59128983 1407419 0.02380252337504266 0.29960862536684996 chr20 63025520 1513497 0.024014034314988594 0.2512967902246085 chr21 48129895 976091 0.020280347588541383 0.23010638102621084 chr22 51304566 944840 0.01841629456528294 0.21331153132846095 chrMT 16571 8401 0.5069700078450304 1.0136346120144488 chrX 155270560 4149305 0.026723063277417174 0.26912411234707834 chrY 59373566 205242 0.0034567908553783007 0.10411883211737488