BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124828.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 23,536,072 number of mapped reads = 23,116,279 (98.22%) number of supplementary alignments = 89,906 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,582,064 number of mapped paired reads (second in pair) = 11,534,215 number of mapped paired reads (both in pair) = 23,027,334 number of mapped paired reads (singletons) = 88,945 number of mapped bases = 2,001,954,212 bp number of sequenced bases = 2,000,816,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,350,791 duplication rate = 12.51% >>>>>>> Insert size mean insert size = 33,484.4452 std insert size = 1,717,006.8403 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.8707 >>>>>>> ACTG content number of A's = 558,096,112 bp (27.89%) number of C's = 375,704,490 bp (18.78%) number of T's = 588,576,178 bp (29.42%) number of G's = 478,420,921 bp (23.91%) number of N's = 18,898 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 14,914,761 number of insertions = 271,266 mapped reads with insertion percentage = 1.14% number of deletions = 673,933 mapped reads with deletion percentage = 2.86% homopolymer indels = 47.52% >>>>>>> Coverage mean coverageData = 0.6467X std coverageData = 4.6299X There is a 25.77% of reference with a coverageData >= 1X There is a 13.58% of reference with a coverageData >= 2X There is a 7.67% of reference with a coverageData >= 3X There is a 4.67% of reference with a coverageData >= 4X There is a 2.97% of reference with a coverageData >= 5X There is a 1.96% of reference with a coverageData >= 6X There is a 1.33% of reference with a coverageData >= 7X There is a 0.93% of reference with a coverageData >= 8X There is a 0.67% of reference with a coverageData >= 9X There is a 0.49% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% 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 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 136052140 0.54584473833668 4.851755090311576 chr2 243199373 175443863 0.7213993228510502 6.143310799334317 chr3 198022430 130292723 0.6579695189075299 1.5834456448620404 chr4 191154276 102638418 0.5369402147195493 4.3769718435129406 chr5 180915260 115452909 0.6381601474635141 1.6464088301408641 chr6 171115067 107337195 0.6272807934557861 2.705545198909685 chr7 159138663 124428478 0.7818871646546384 7.448636780198559 chr8 146364022 107059545 0.731460802573463 3.388366858098803 chr9 141213431 96074403 0.680348903922602 5.651897029143792 chr10 135534747 95486808 0.7045190264013995 9.172893999156802 chr11 135006516 117325431 0.8690353212284954 4.066954039282059 chr12 133851895 114558917 0.8558632434751857 1.9162104635469988 chr13 115169878 37983084 0.3298005056495762 1.0480426293262612 chr14 107349540 58204695 0.5421978985657507 1.7547733269181929 chr15 102531392 56163485 0.5477686775187837 1.470805820938157 chr16 90354753 55754268 0.6170596028301909 6.820485091369623 chr17 81195210 71873401 0.8851926240476501 7.811563568232954 chr18 78077248 52313035 0.670016379163364 5.9284829681636415 chr19 59128983 30593353 0.5174002908184637 2.7899798839788033 chr20 63025520 33067956 0.5246756551949115 1.7693405012747623 chr21 48129895 24734187 0.5139048610016705 2.2240393697857668 chr22 51304566 22331017 0.4352637346157455 1.472121811538095 chrMT 16571 224965 13.575825236859574 8.041524431234958 chrX 155270560 131783397 0.8487339583241021 2.7276372953928196 chrY 59373566 4776539 0.0804489155999153 4.933040199059022