BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975340.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,634,616 number of mapped reads = 4,594,331 (99.13%) number of supplementary alignments = 11,363 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,297,005 number of mapped paired reads (second in pair) = 2,297,326 number of mapped paired reads (both in pair) = 4,588,620 number of mapped paired reads (singletons) = 5,711 number of mapped bases = 448,241,713 bp number of sequenced bases = 448,118,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,870 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 41,442.1051 std insert size = 1,982,263.1928 median insert size = 160 >>>>>>> Mapping quality mean mapping quality = 53.7548 >>>>>>> ACTG content number of A's = 136,375,167 bp (30.43%) number of C's = 89,007,403 bp (19.86%) number of T's = 133,637,470 bp (29.82%) number of G's = 89,089,359 bp (19.88%) number of N's = 8,925 bp (0%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,771,553 number of insertions = 57,065 mapped reads with insertion percentage = 1.22% number of deletions = 53,618 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.81% >>>>>>> Coverage mean coverageData = 0.1448X std coverageData = 0.9422X There is a 10.76% of reference with a coverageData >= 1X There is a 3.03% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.02% 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% 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 35387666 0.14197624005117324 2.347691629718241 chr2 243199373 40484719 0.16646720137720092 0.6437632392762167 chr3 198022430 32760120 0.16543641041067925 0.4859884931185233 chr4 191154276 34942749 0.18279867827806268 0.7464143197174752 chr5 180915260 30255272 0.16723449420463482 0.4890927790381773 chr6 171115067 28692263 0.16767817996997308 0.6543495832643209 chr7 159138663 25216194 0.15845422805896012 0.7388879812117096 chr8 146364022 23898658 0.16328232630830547 0.633039537846446 chr9 141213431 19125668 0.1354380235970614 0.9512459598775034 chr10 135534747 21394758 0.1578544135254113 1.4190574238920255 chr11 135006516 20066426 0.14863301857222952 0.544208045139091 chr12 133851895 20491385 0.153089988005026 0.46919296900806023 chr13 115169878 16977525 0.14741289384712208 0.45759724135032304 chr14 107349540 14064179 0.13101294146206868 0.43610090203602686 chr15 102531392 12002234 0.11705911492940621 0.40799572158045805 chr16 90354753 10376247 0.11483897255521246 0.5551068699808575 chr17 81195210 9409735 0.1158902723448834 0.5320033537401633 chr18 78077248 13249869 0.16970204943698836 1.1436791531090968 chr19 59128983 5272660 0.08917217466770906 0.9567874275978535 chr20 63025520 7719551 0.1224829402438885 0.44332038392976675 chr21 48129895 6480181 0.13463941693618903 0.6226622375718943 chr22 51304566 3663488 0.07140666583165327 0.604609822219717 chrMT 16571 376837 22.740751915997826 7.985928218406948 chrX 155270560 12531161 0.08070532495020305 0.37230283349160087 chrY 59373566 3402168 0.0573010554899128 0.7790538351116989