BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094081.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 391,544 number of mapped reads = 380,891 (97.28%) number of supplementary alignments = 13,084 (3.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 191,437 number of mapped paired reads (second in pair) = 189,454 number of mapped paired reads (both in pair) = 378,126 number of mapped paired reads (singletons) = 2,765 number of mapped bases = 51,236,310 bp number of sequenced bases = 50,148,007 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 363,118 duplication rate = 48.62% >>>>>>> Insert size mean insert size = 392,961.3625 std insert size = 5,664,478.2768 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 39.4849 >>>>>>> ACTG content number of A's = 13,127,247 bp (26.18%) number of C's = 11,974,006 bp (23.88%) number of T's = 12,608,465 bp (25.14%) number of G's = 12,437,721 bp (24.8%) number of N's = 568 bp (0%) GC percentage = 48.68% >>>>>>> Mismatches and indels general error rate = 0.0389 number of mismatches = 1,879,097 number of insertions = 29,189 mapped reads with insertion percentage = 7.53% number of deletions = 143,653 mapped reads with deletion percentage = 36.11% homopolymer indels = 28.46% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 4.7285X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% 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 0.01% 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% 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 302057 0.0012118605714526987 0.5661385646468294 chr2 243199373 2218492 0.009122112333735334 3.8412524655595663 chr3 198022430 1274663 0.006436962721849237 3.0440867777111618 chr4 191154276 767156 0.004013281921038481 1.6377887041495138 chr5 180915260 417231 0.0023062233666745415 1.077589519956166 chr6 171115067 1129036 0.006598109797075906 3.8230586278141803 chr7 159138663 1620964 0.010185859108292245 3.8389512136484973 chr8 146364022 1077471 0.007361583709417332 3.0584830485611945 chr9 141213431 570525 0.004040161024060098 2.07475023581768 chr10 135534747 1011530 0.007463252209413133 2.646402464431585 chr11 135006516 1767370 0.013090997770803893 4.346057431180659 chr12 133851895 1748690 0.013064364908692552 5.298363664480764 chr13 115169878 1509421 0.01310603975806938 4.008664561952784 chr14 107349540 311860 0.0029050892998703113 1.329828390468474 chr15 102531392 891197 0.008691942853950524 2.585621037824728 chr16 90354753 279312 0.003091281761347961 0.9692584675941743 chr17 81195210 1274138 0.015692280369741022 4.995313710194618 chr18 78077248 151052 0.0019346481064496535 0.6247730506640861 chr19 59128983 192549 0.0032564233347290956 0.7638053014326383 chr20 63025520 349243 0.005541295018271964 1.8240459154461313 chr21 48129895 874059 0.018160417761144087 7.991779325733594 chr22 51304566 62446 0.0012171626205745509 0.27578603346367314 chrMT 16571 1897527 114.50890109226962 548.136481997234 chrX 155270560 29170286 0.18786746180344813 15.10511577451258 chrY 59373566 368035 0.006198633917322736 1.2502243088936031