BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093988.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 = 336,586 number of mapped reads = 322,671 (95.87%) number of supplementary alignments = 19,597 (5.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 162,357 number of mapped paired reads (second in pair) = 160,314 number of mapped paired reads (both in pair) = 319,498 number of mapped paired reads (singletons) = 3,173 number of mapped bases = 41,871,799 bp number of sequenced bases = 41,130,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 302,765 duplication rate = 48.88% >>>>>>> Insert size mean insert size = 986,813.544 std insert size = 9,035,008.4212 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 39.6993 >>>>>>> ACTG content number of A's = 10,816,941 bp (26.3%) number of C's = 9,669,960 bp (23.51%) number of T's = 10,241,980 bp (24.9%) number of G's = 10,401,500 bp (25.29%) number of N's = 383 bp (0%) GC percentage = 48.8% >>>>>>> Mismatches and indels general error rate = 0.0349 number of mismatches = 1,393,039 number of insertions = 20,874 mapped reads with insertion percentage = 6.34% number of deletions = 109,746 mapped reads with deletion percentage = 32.62% homopolymer indels = 31.01% >>>>>>> Coverage mean coverageData = 0.0135X std coverageData = 2.6946X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 872668 0.0035011668035121964 1.1335472939658517 chr2 243199373 2057897 0.008461769348393839 2.7745439413524506 chr3 198022430 687862 0.003473656999361133 1.17212387217345 chr4 191154276 896278 0.004688767726022514 2.038154013944349 chr5 180915260 264518 0.0014621099403112816 0.7391825824977796 chr6 171115067 908745 0.0053107246248514164 1.6332887974453207 chr7 159138663 861469 0.005413323096726029 1.7192531676023783 chr8 146364022 487158 0.003328399926041934 1.141540624955283 chr9 141213431 450201 0.0031880890989752953 0.9185227558864586 chr10 135534747 671471 0.0049542350936767525 1.5364670026822025 chr11 135006516 972970 0.0072068373351698075 1.8462457851288099 chr12 133851895 897914 0.006708265131397654 1.6221200568210543 chr13 115169878 911544 0.00791477785536944 2.101887415285874 chr14 107349540 150375 0.0014007978050022385 0.5002450988090166 chr15 102531392 563069 0.005491674198668833 1.5570849277724614 chr16 90354753 260220 0.0028799813109997656 0.7486699432452725 chr17 81195210 1138984 0.014027724049238865 3.4313517863201906 chr18 78077248 201552 0.0025814434443181193 0.6855756143649765 chr19 59128983 174084 0.002944139932188585 0.706069439887263 chr20 63025520 284771 0.004518344315128221 1.577301245304956 chr21 48129895 92578 0.0019235030535595392 0.36273613073778105 chr22 51304566 131283 0.00255889505039376 0.6963205712516068 chrMT 16571 1277369 77.08460563635266 327.1411733672857 chrX 155270560 25943367 0.16708490650127109 9.017690259736085 chrY 59373566 713452 0.012016323897405791 1.8514602165573737