BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006074.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 5,076,894 number of mapped reads = 4,407,122 (86.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,234,015 number of mapped paired reads (second in pair) = 2,173,107 number of mapped paired reads (both in pair) = 4,018,184 number of mapped paired reads (singletons) = 388,938 number of mapped bases = 169,956,325 bp number of sequenced bases = 169,937,071 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,384 duplication rate = 4.01% >>>>>>> Insert size mean insert size = 63,226.0148 std insert size = 2,485,005.1231 median insert size = 88 >>>>>>> Mapping quality mean mapping quality = 46.294 >>>>>>> ACTG content number of A's = 44,760,524 bp (26.34%) number of C's = 38,325,194 bp (22.55%) number of T's = 46,232,275 bp (27.21%) number of G's = 40,612,253 bp (23.9%) number of N's = 6,825 bp (0%) GC percentage = 46.45% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 784,863 number of insertions = 5,827 mapped reads with insertion percentage = 0.13% number of deletions = 15,047 mapped reads with deletion percentage = 0.34% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.0549X std coverageData = 0.3553X There is a 3.68% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 14721103 0.059061449640279935 0.3784418869501618 chr2 243199373 14836345 0.06100486533737898 0.38960132177722395 chr3 198022430 11147154 0.056292380615670656 0.3283620197145969 chr4 191154276 10063846 0.05264776813049162 0.32962469964371277 chr5 180915260 9875967 0.05458891085251736 0.3245908156663724 chr6 171115067 9095777 0.053155909409193056 0.3479596210587108 chr7 159138663 9493795 0.05965737565609685 0.4119008572216852 chr8 146364022 8076307 0.055179591880851704 0.35087298843690395 chr9 141213431 7590441 0.05375155143705842 0.3328533660510239 chr10 135534747 8452315 0.0623627164774211 0.3615309959323251 chr11 135006516 7775101 0.05759056103632806 0.4883675240386564 chr12 133851895 7681145 0.0573854034715011 0.3360326429981969 chr13 115169878 5308989 0.04609702721053503 0.30054749518187857 chr14 107349540 5315436 0.04951521916162845 0.31457300704416585 chr15 102531392 5355547 0.05223324189337057 0.32153928003773125 chr16 90354753 5737227 0.06349668179603125 0.3798537502371069 chr17 81195210 5405809 0.06657792990497838 0.3798287416963331 chr18 78077248 4384341 0.0561538874935756 0.37286994383816763 chr19 59128983 4271204 0.0722353705965144 0.4281590241964347 chr20 63025520 4198236 0.06661168364814761 0.36763683872768493 chr21 48129895 2366333 0.04916555500484678 0.3356956658358025 chr22 51304566 2658495 0.051817902523529774 0.3435363288223708 chrMT 16571 3993 0.24096312835676784 0.597417457911003 chrX 155270560 5001342 0.03221049759851449 0.2504906990366843 chrY 59373566 1140077 0.0192017605949422 0.2057726615829177