BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124932.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 = 7,153,068 number of mapped reads = 7,078,208 (98.95%) number of supplementary alignments = 33,916 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,541,468 number of mapped paired reads (second in pair) = 3,536,740 number of mapped paired reads (both in pair) = 7,054,134 number of mapped paired reads (singletons) = 24,074 number of mapped bases = 645,943,613 bp number of sequenced bases = 645,590,351 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 408,614 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 69,468.4732 std insert size = 2,516,849.459 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 52.8519 >>>>>>> ACTG content number of A's = 186,896,435 bp (28.95%) number of C's = 130,919,818 bp (20.28%) number of T's = 186,925,890 bp (28.95%) number of G's = 140,837,628 bp (21.82%) number of N's = 10,580 bp (0%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 4,650,771 number of insertions = 107,914 mapped reads with insertion percentage = 1.49% number of deletions = 204,190 mapped reads with deletion percentage = 2.83% homopolymer indels = 45.82% >>>>>>> Coverage mean coverageData = 0.2087X std coverageData = 2.0106X There is a 13.35% of reference with a coverageData >= 1X There is a 4.53% of reference with a coverageData >= 2X There is a 1.34% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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% 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 53873959 0.2161437302898435 2.38799283796677 chr2 243199373 59244266 0.24360369547498792 2.5348991695194343 chr3 198022430 43489753 0.21962033795868477 0.6630331863895103 chr4 191154276 34337124 0.17963042584514302 1.3549760093190633 chr5 180915260 37159753 0.20539866565153211 0.6326708215229198 chr6 171115067 33176020 0.19388134885866012 1.7820700388192474 chr7 159138663 40363014 0.25363424097637416 2.5469250250540143 chr8 146364022 30252553 0.20669391689714567 0.8599614858433293 chr9 141213431 27744977 0.19647548256227837 2.9130311734126755 chr10 135534747 33480867 0.2470279226625184 4.845530472823684 chr11 135006516 31920299 0.2364352473179887 1.5002248385953405 chr12 133851895 28654732 0.21407789557256549 0.6325473532581226 chr13 115169878 19784150 0.17178233009850025 0.5563389860883671 chr14 107349540 19227094 0.17910737204835717 0.6793663047701559 chr15 102531392 20374188 0.1987117077275221 0.6105563469422745 chr16 90354753 23284729 0.25770342153444875 3.2039120671946484 chr17 81195210 15505736 0.19096860516771863 1.6421847127945328 chr18 78077248 17270177 0.22119346470818232 3.07203979381631 chr19 59128983 10402339 0.17592622893581647 1.4217997621483363 chr20 63025520 14200866 0.22531929922989927 0.7403646539030471 chr21 48129895 7986597 0.1659383840334578 0.8414051400013046 chr22 51304566 7570466 0.14755930300628603 0.5660222230915553 chrMT 16571 157215 9.487357431657715 5.704207063431609 chrX 155270560 34574822 0.22267467831635307 1.104871299759172 chrY 59373566 1907917 0.03213411503698464 1.7950970799128418