BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1954922.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 15,390,318 number of mapped reads = 15,041,202 (97.73%) number of supplementary alignments = 28,186 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,633,860 number of mapped paired reads (second in pair) = 7,407,342 number of mapped paired reads (both in pair) = 14,792,316 number of mapped paired reads (singletons) = 248,886 number of mapped bases = 1,406,883,440 bp number of sequenced bases = 1,405,960,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 659,699 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 32,841.8838 std insert size = 1,833,951.1642 median insert size = 356 >>>>>>> Mapping quality mean mapping quality = 54.3133 >>>>>>> ACTG content number of A's = 402,191,153 bp (28.61%) number of C's = 278,892,717 bp (19.84%) number of T's = 401,917,896 bp (28.59%) number of G's = 322,920,917 bp (22.97%) number of N's = 37,654 bp (0%) GC percentage = 42.8% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 11,722,269 number of insertions = 235,087 mapped reads with insertion percentage = 1.54% number of deletions = 671,697 mapped reads with deletion percentage = 4.36% homopolymer indels = 54.25% >>>>>>> Coverage mean coverageData = 0.4545X std coverageData = 1.3268X There is a 23.75% of reference with a coverageData >= 1X There is a 9.99% of reference with a coverageData >= 2X There is a 4.88% of reference with a coverageData >= 3X There is a 2.61% of reference with a coverageData >= 4X There is a 1.48% of reference with a coverageData >= 5X There is a 0.88% of reference with a coverageData >= 6X There is a 0.55% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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% 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 119537102 0.47958597463233604 1.4179345163971926 chr2 243199373 122412517 0.5033422392910528 2.1604920549282016 chr3 198022430 96124479 0.4854221766695823 1.1438981081392119 chr4 191154276 80384025 0.4205191046838 1.1369361930206654 chr5 180915260 87923857 0.48599469718585375 1.1444042852562792 chr6 171115067 79465224 0.4643964169443945 1.1250748921638087 chr7 159138663 71211601 0.4474814583555977 1.1231131532524967 chr8 146364022 72932418 0.4982947107042467 1.2186977952276623 chr9 141213431 60794327 0.43051377315518946 1.4364080246374178 chr10 135534747 69628688 0.5137331167187703 1.2861261278007323 chr11 135006516 69435562 0.5143126721379878 1.3323828732232104 chr12 133851895 64917932 0.48499822882597216 1.1672791682673445 chr13 115169878 41528715 0.3605866023405877 0.9752603566361446 chr14 107349540 64484257 0.600694301997009 1.4439008686211512 chr15 102531392 41709068 0.4067931507259747 1.0881665348815674 chr16 90354753 44219044 0.48939366808960233 1.5378785462336702 chr17 81195210 38379544 0.47268236636126687 1.2349390424283921 chr18 78077248 37729481 0.4832327210098389 1.6148818293529406 chr19 59128983 22376505 0.37843547892579177 1.1322453662749195 chr20 63025520 35695624 0.5663677824474911 1.3227695327271312 chr21 48129895 19306213 0.4011272619647311 1.4740490990624138 chr22 51304566 18643776 0.36339408854954547 1.071167860105055 chrMT 16571 227913 13.75372638947559 10.890176743079184 chrX 155270560 40312438 0.2596270535766729 0.7662603624372363 chrY 59373566 7503130 0.1263715573358016 0.7760154949451247