BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714262.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 227,728 number of mapped reads = 218,506 (95.95%) number of supplementary alignments = 6,741 (2.96%) number of secondary alignments = 0 number of mapped bases = 28,224,160 bp number of sequenced bases = 27,691,909 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,312 duplication rate = 40.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9921 >>>>>>> ACTG content number of A's = 8,123,674 bp (29.34%) number of C's = 5,678,640 bp (20.51%) number of T's = 7,735,306 bp (27.93%) number of G's = 6,154,055 bp (22.22%) number of N's = 234 bp (0%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0412 number of mismatches = 1,046,968 number of insertions = 30,725 mapped reads with insertion percentage = 13.71% number of deletions = 89,720 mapped reads with deletion percentage = 39.2% homopolymer indels = 27.54% >>>>>>> Coverage mean coverageData = 0.0091X std coverageData = 1.5608X There is a 0.04% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 2175481 0.008728086579170449 1.5751084718716353 chr2 243199373 2826987 0.011624154146153988 2.082608959542898 chr3 198022430 1859967 0.009392708694666558 1.1751756921470529 chr4 191154276 1825066 0.009547607504212985 1.767339759711298 chr5 180915260 1788276 0.009884605643548256 1.8046289787296326 chr6 171115067 1504514 0.008792411015448453 1.3219764054858143 chr7 159138663 1126826 0.007080780865929482 1.018880021695864 chr8 146364022 1425204 0.009737392977626701 1.4211148235436992 chr9 141213431 1489497 0.010547842294122858 1.971450945344861 chr10 135534747 1069069 0.00788778541048223 1.1634450831588476 chr11 135006516 993330 0.0073576448710075595 1.2258174079726158 chr12 133851895 1573121 0.01175269875708521 1.847839277042449 chr13 115169878 1222973 0.010618861643666933 1.8231037663781249 chr14 107349540 1188198 0.011068496427651203 2.250277499173882 chr15 102531392 768921 0.0074993715095568 1.0260864314747655 chr16 90354753 563136 0.00623250002133258 0.9406051050939476 chr17 81195210 308365 0.003797822556281337 0.6690193567340657 chr18 78077248 952123 0.012194628068858165 2.537715431051846 chr19 59128983 206794 0.003497337337934596 0.6164493579422597 chr20 63025520 473523 0.007513194655117483 1.2761860349142502 chr21 48129895 296195 0.006154075341323724 0.968487674592137 chr22 51304566 344832 0.006721273112416544 1.6207416409090944 chrMT 16571 0 0.0 0.0 chrX 155270560 2164730 0.013941664150628426 1.369834819442757 chrY 59373566 77032 0.0012974123871892754 0.34362466911328066