BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819045.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 555,476 number of mapped reads = 485,479 (87.4%) number of supplementary alignments = 2,073 (0.37%) number of secondary alignments = 0 number of mapped bases = 27,422,285 bp number of sequenced bases = 27,414,832 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,321 duplication rate = 1.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4218 >>>>>>> ACTG content number of A's = 6,895,865 bp (25.15%) number of C's = 5,256,087 bp (19.17%) number of T's = 8,646,553 bp (31.54%) number of G's = 6,615,705 bp (24.13%) number of N's = 622 bp (0%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 136,163 number of insertions = 1,905 mapped reads with insertion percentage = 0.39% number of deletions = 4,264 mapped reads with deletion percentage = 0.87% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.0089X std coverageData = 0.107X There is a 0.84% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2970964 0.011919585147192071 0.13735666820576334 chr2 243199373 1660264 0.006826761021295889 0.10715387398849761 chr3 198022430 1855815 0.009371741372934369 0.10040278744813315 chr4 191154276 1751652 0.009163551224980183 0.10425320894050645 chr5 180915260 1311504 0.007249272394158459 0.08836511464546472 chr6 171115067 1294087 0.0075626712637759715 0.09206699967150572 chr7 159138663 1337324 0.008403514110207146 0.10161835920496158 chr8 146364022 1994208 0.013624987703603826 0.1253088765609319 chr9 141213431 923084 0.006536800313278982 0.09745724833855288 chr10 135534747 1463739 0.010799732411054709 0.12755644468485897 chr11 135006516 949003 0.0070293125703651226 0.09512035758418388 chr12 133851895 1440756 0.010763807266232578 0.1070409966897544 chr13 115169878 874529 0.007593383054551816 0.08982628399553227 chr14 107349540 688613 0.006414680491411514 0.08614418571340678 chr15 102531392 641854 0.006260073012565752 0.08162518042258605 chr16 90354753 909000 0.010060345137571236 0.10832040283657737 chr17 81195210 664036 0.008178265688333092 0.09434119984488723 chr18 78077248 619769 0.00793789504466141 0.1468118236095832 chr19 59128983 588170 0.009947236873666507 0.12170330279220318 chr20 63025520 832184 0.01320392120525146 0.12191258163309758 chr21 48129895 382803 0.007953539063403316 0.09716136611916386 chr22 51304566 389673 0.007595288887152851 0.09003089806660064 chrMT 16571 2373 0.14320197936153523 0.368953435480829 chrX 155270560 1778680 0.011455358955361532 0.11488675346030076 chrY 59373566 98201 0.0016539515244881871 0.05245335459458833