BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094022.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 = 720,980 number of mapped reads = 662,202 (91.85%) number of supplementary alignments = 32,715 (4.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 332,803 number of mapped paired reads (second in pair) = 329,399 number of mapped paired reads (both in pair) = 654,854 number of mapped paired reads (singletons) = 7,348 number of mapped bases = 84,117,340 bp number of sequenced bases = 82,288,934 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 629,662 duplication rate = 48.17% >>>>>>> Insert size mean insert size = 602,526.6223 std insert size = 7,050,990.2355 median insert size = 160 >>>>>>> Mapping quality mean mapping quality = 45.2102 >>>>>>> ACTG content number of A's = 22,844,282 bp (27.76%) number of C's = 18,395,215 bp (22.35%) number of T's = 21,727,299 bp (26.4%) number of G's = 19,321,294 bp (23.48%) number of N's = 844 bp (0%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.039 number of mismatches = 3,114,288 number of insertions = 50,170 mapped reads with insertion percentage = 7.46% number of deletions = 242,061 mapped reads with deletion percentage = 35.22% homopolymer indels = 29.05% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 7.117X There is a 0.04% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1480566 0.00594006945322716 1.7471603281195396 chr2 243199373 4341140 0.017850128256704016 4.422524805683394 chr3 198022430 1196710 0.00604330529627376 1.6203584164335672 chr4 191154276 800145 0.004185859802581659 1.0855204260918239 chr5 180915260 1609007 0.008893705262894904 3.075113117360266 chr6 171115067 1653398 0.009662492198889767 3.551110409283858 chr7 159138663 2594919 0.01630602489100967 4.367611267261962 chr8 146364022 1167608 0.007977424943952415 1.9913168896782198 chr9 141213431 835561 0.005917007993382726 1.3685302627905689 chr10 135534747 928578 0.006851217274932457 1.3633465343096505 chr11 135006516 2263971 0.016769346155114467 3.634093933779703 chr12 133851895 2091662 0.0156266894839255 3.604209002105325 chr13 115169878 2139116 0.018573571815366514 4.27957215493181 chr14 107349540 510528 0.004755753960380268 0.9882460397671834 chr15 102531392 1003843 0.00979059174384368 2.999921285458236 chr16 90354753 532293 0.005891145538298356 1.5758827937886735 chr17 81195210 2035251 0.025066146143350083 5.040804723238097 chr18 78077248 747143 0.009569279388535825 3.1684944247327262 chr19 59128983 331250 0.0056021596041995175 1.228797540492686 chr20 63025520 446556 0.007085320359118021 1.949412472116753 chr21 48129895 462412 0.00960758381043632 2.859367140416955 chr22 51304566 299519 0.005838057376803461 1.0057123525462175 chrMT 16571 8195217 494.5517470279404 2139.3573260446374 chrX 155270560 45641994 0.2939513710776853 18.164450758169767 chrY 59373566 808953 0.013624800639395652 3.8990143817951144