BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094010.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 = 443,372 number of mapped reads = 394,946 (89.08%) number of supplementary alignments = 2,772 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 197,993 number of mapped paired reads (second in pair) = 196,953 number of mapped paired reads (both in pair) = 392,534 number of mapped paired reads (singletons) = 2,412 number of mapped bases = 54,483,051 bp number of sequenced bases = 53,633,404 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 387,308 duplication rate = 46.24% >>>>>>> Insert size mean insert size = 54,297.8955 std insert size = 2,164,567.6392 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 33.3786 >>>>>>> ACTG content number of A's = 15,057,441 bp (28.07%) number of C's = 11,773,954 bp (21.95%) number of T's = 14,642,142 bp (27.3%) number of G's = 12,159,266 bp (22.67%) number of N's = 601 bp (0%) GC percentage = 44.62% >>>>>>> Mismatches and indels general error rate = 0.0324 number of mismatches = 1,731,301 number of insertions = 12,898 mapped reads with insertion percentage = 3.17% number of deletions = 133,907 mapped reads with deletion percentage = 32.42% homopolymer indels = 28.57% >>>>>>> Coverage mean coverageData = 0.0176X std coverageData = 18.5171X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 1016743 0.004079199465665524 2.938140047320884 chr2 243199373 4273678 0.017572734449442844 16.657030477630357 chr3 198022430 255038 0.0012879248073059198 1.0605324915722456 chr4 191154276 824025 0.004310785074983099 2.138080644101553 chr5 180915260 1535225 0.00848587896897144 5.734814557324357 chr6 171115067 209951 0.0012269579978015613 0.5707810668597539 chr7 159138663 1341297 0.008428479759189632 6.551937141913557 chr8 146364022 227434 0.001553892800240212 0.5855354330581017 chr9 141213431 497945 0.0035261872505597575 2.079879048774056 chr10 135534747 780653 0.005759799736078011 4.1039051214301185 chr11 135006516 788750 0.005842310603734119 3.59478481901017 chr12 133851895 170282 0.0012721672711469643 0.5874106609050217 chr13 115169878 48230 4.1877269332524605E-4 0.1574052800429622 chr14 107349540 499043 0.004648767009155326 1.7440744209656356 chr15 102531392 197418 0.0019254395765932837 0.8242599956347193 chr16 90354753 32999 3.6521598371255575E-4 0.12992355444503342 chr17 81195210 70440 8.675388609746806E-4 0.2972123777700865 chr18 78077248 123536 0.0015822278981964118 0.8258206714170949 chr19 59128983 57192 9.672413949686908E-4 0.2880891668440445 chr20 63025520 57562 9.133125756042949E-4 0.49799208878400564 chr21 48129895 14613 3.0361587117528515E-4 0.049702804799715644 chr22 51304566 56470 0.0011006817599821428 0.26781465384291175 chrMT 16571 21406656 1291.8143745096856 6955.215598836099 chrX 155270560 19991038 0.12874969987871493 30.393965336395773 chrY 59373566 6833 1.1508488474483746E-4 0.06104004938311179