BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080966.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 7,236,381 number of mapped reads = 6,484,026 (89.6%) number of supplementary alignments = 78,776 (1.09%) number of secondary alignments = 0 number of mapped bases = 441,497,608 bp number of sequenced bases = 441,336,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 583,737 duplication rate = 7.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1798 >>>>>>> ACTG content number of A's = 126,368,833 bp (28.63%) number of C's = 79,568,164 bp (18.03%) number of T's = 141,526,352 bp (32.07%) number of G's = 92,999,494 bp (21.07%) number of N's = 874,130 bp (0.2%) GC percentage = 39.1% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 4,456,260 number of insertions = 34,815 mapped reads with insertion percentage = 0.53% number of deletions = 97,514 mapped reads with deletion percentage = 1.49% homopolymer indels = 49.23% >>>>>>> Coverage mean coverageData = 0.1426X std coverageData = 0.8732X There is a 8.24% of reference with a coverageData >= 1X There is a 3.26% of reference with a coverageData >= 2X There is a 1.37% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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% 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 35926805 0.14413927979742125 1.0149497167081554 chr2 243199373 28632460 0.11773245813425678 0.8117625048224961 chr3 198022430 38014546 0.1919709095580738 0.6879719857303723 chr4 191154276 28483939 0.1490102109983666 0.6357339297194927 chr5 180915260 25720128 0.1421667138526623 0.5817899996329441 chr6 171115067 37803786 0.2209261093296945 1.1011789287820237 chr7 159138663 21743243 0.13663080102664932 0.8551094749686617 chr8 146364022 34540824 0.23599258566425566 1.8174050983513204 chr9 141213431 22594385 0.16000167151239317 1.053701021302012 chr10 135534747 20298829 0.14976845015249116 0.7364074485406007 chr11 135006516 19190502 0.14214500580105333 0.7197046646668235 chr12 133851895 21822510 0.16303474821929118 0.6551155172582199 chr13 115169878 12032408 0.10447530386374118 0.49769175783933267 chr14 107349540 12578418 0.1171725374882836 0.7030330742356297 chr15 102531392 11597052 0.1131073300945724 0.5233073647382002 chr16 90354753 9952195 0.11014578281233307 0.6368292373484017 chr17 81195210 9072041 0.11173123389914258 0.5377240350737851 chr18 78077248 11070392 0.14178768186091806 1.6815380295821456 chr19 59128983 7779286 0.13156468461498821 0.9297530276656234 chr20 63025520 6896690 0.10942694324457775 0.5475105024988162 chr21 48129895 7944819 0.16507035803838757 0.752077751943162 chr22 51304566 3598949 0.07014870762185182 0.3995408140435811 chrMT 16571 81014 4.888902299197393 4.027002064634148 chrX 155270560 13216398 0.08511850540115268 0.5013497090846674 chrY 59373566 905989 0.015259130637361415 0.29494658197873524