BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094068.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 = 357,716 number of mapped reads = 348,147 (97.32%) number of supplementary alignments = 12,970 (3.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 174,919 number of mapped paired reads (second in pair) = 173,228 number of mapped paired reads (both in pair) = 345,564 number of mapped paired reads (singletons) = 2,583 number of mapped bases = 47,345,717 bp number of sequenced bases = 46,327,864 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 331,238 duplication rate = 49.38% >>>>>>> Insert size mean insert size = 482,669.8245 std insert size = 6,338,467.8611 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 38.0448 >>>>>>> ACTG content number of A's = 12,069,203 bp (26.05%) number of C's = 11,077,309 bp (23.91%) number of T's = 11,598,252 bp (25.04%) number of G's = 11,582,626 bp (25%) number of N's = 474 bp (0%) GC percentage = 48.91% >>>>>>> Mismatches and indels general error rate = 0.0404 number of mismatches = 1,802,913 number of insertions = 29,360 mapped reads with insertion percentage = 8.3% number of deletions = 137,730 mapped reads with deletion percentage = 37.71% homopolymer indels = 28.93% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 4.3141X 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% 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 302527 0.0012137462237255569 0.5069325355732825 chr2 243199373 2279332 0.00937227745237649 4.150067784921049 chr3 198022430 839264 0.004238226952371002 1.6209627369314938 chr4 191154276 572632 0.0029956536258702367 1.2407774488863643 chr5 180915260 326972 0.001807321284008878 0.9000419835200163 chr6 171115067 1071674 0.006262885079547086 3.405994130770588 chr7 159138663 1464449 0.009202345755537735 3.3872139034064097 chr8 146364022 653340 0.004463801903448649 1.5921427515286506 chr9 141213431 501307 0.003549995184239947 1.7214280216556819 chr10 135534747 962210 0.0070993602843409595 2.4286558931993887 chr11 135006516 1611059 0.011933194394854246 3.4999063228307508 chr12 133851895 1290370 0.00964028189514986 3.9239692430823285 chr13 115169878 1206778 0.010478243278159938 3.0578839374608546 chr14 107349540 233988 0.0021796833037197923 0.9601927371236588 chr15 102531392 810170 0.00790167756622284 2.6013500288525546 chr16 90354753 287831 0.003185565677989292 1.0732388464803886 chr17 81195210 946375 0.01165555209476027 4.031077236006728 chr18 78077248 123324 0.0015795126385602116 0.45437124025503295 chr19 59128983 192284 0.003251941607045736 0.8313272507136142 chr20 63025520 306175 0.0048579527784935374 1.7873541310293446 chr21 48129895 694821 0.014436370575917524 6.5678716583540755 chr22 51304566 47140 9.188266011255216E-4 0.22170397563008598 chrMT 16571 1305201 78.76416631464606 378.42063533663253 chrX 155270560 28965259 0.18654701187398307 15.026916336685433 chrY 59373566 351235 0.00591567971511093 1.3949836441338432