BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046405.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 5,935,574 number of mapped reads = 5,845,428 (98.48%) number of supplementary alignments = 12,290 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,956,204 number of mapped paired reads (second in pair) = 2,889,224 number of mapped paired reads (both in pair) = 5,770,142 number of mapped paired reads (singletons) = 75,286 number of mapped bases = 557,006,411 bp number of sequenced bases = 556,853,206 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,521,198 duplication rate = 45.07% >>>>>>> Insert size mean insert size = 23,258.5021 std insert size = 1,540,817.8998 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 53.2626 >>>>>>> ACTG content number of A's = 161,571,596 bp (29.02%) number of C's = 117,479,059 bp (21.1%) number of T's = 160,357,568 bp (28.8%) number of G's = 117,399,188 bp (21.08%) number of N's = 45,795 bp (0.01%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 2,020,104 number of insertions = 39,085 mapped reads with insertion percentage = 0.65% number of deletions = 55,740 mapped reads with deletion percentage = 0.92% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.1799X std coverageData = 7.432X There is a 2.15% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 73340374 0.2942434955859147 9.885731180305738 chr2 243199373 52900199 0.2175178264131462 8.409873022263513 chr3 198022430 33294448 0.16813473099991755 7.075265266340719 chr4 191154276 16797373 0.08787338348633122 3.8056550654774113 chr5 180915260 31553571 0.1744107766254765 6.873914468319212 chr6 171115067 35932583 0.20999076019413299 6.929451467130464 chr7 159138663 37505728 0.23567954696213578 7.971541703109968 chr8 146364022 48604638 0.3320805026798184 12.189385513532633 chr9 141213431 14232143 0.10078462720730863 4.552055965599737 chr10 135534747 17022775 0.12559712824047992 5.248303301488225 chr11 135006516 16541613 0.12252455281491746 4.869625458432654 chr12 133851895 17429705 0.1302163484499043 5.13358833311407 chr13 115169878 15437129 0.13403790355669215 5.714144265189185 chr14 107349540 26979017 0.25131935358083507 10.669298188796919 chr15 102531392 11884695 0.11591274406964064 5.455439374671754 chr16 90354753 26529355 0.2936132756624325 11.599020886483219 chr17 81195210 33765596 0.4158569945197506 12.197522437220332 chr18 78077248 6109059 0.07824377980125528 3.2582937815180006 chr19 59128983 8474689 0.14332546527986115 4.037667162258712 chr20 63025520 11723365 0.18600980999442765 8.76492124998324 chr21 48129895 3226407 0.06703540491829454 5.005482689837167 chr22 51304566 7300602 0.1422992643578741 5.8039903222683815 chrMT 16571 381245 23.00675879548609 7.051776770181084 chrX 155270560 9782011 0.06299977922408471 3.4622139512625254 chrY 59373566 258091 0.004346900773990903 0.2218256216498382