BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080685.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,156,003 number of mapped reads = 1,069,047 (92.48%) number of supplementary alignments = 9,628 (0.83%) number of secondary alignments = 0 number of mapped bases = 71,839,130 bp number of sequenced bases = 71,811,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,487 duplication rate = 2.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2984 >>>>>>> ACTG content number of A's = 19,853,372 bp (27.65%) number of C's = 13,200,437 bp (18.38%) number of T's = 22,829,858 bp (31.79%) number of G's = 15,925,041 bp (22.18%) number of N's = 3,278 bp (0%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 482,986 number of insertions = 5,435 mapped reads with insertion percentage = 0.5% number of deletions = 16,730 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.1926X There is a 2.07% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 8925762 0.03581039021764363 0.23174697079065906 chr2 243199373 4802369 0.019746633968501227 0.25294292091001397 chr3 198022430 4573982 0.023098302550877695 0.16605623561203015 chr4 191154276 3097189 0.016202561955768125 0.1414639455620474 chr5 180915260 3247530 0.017950558731198243 0.1465664046031511 chr6 171115067 4386134 0.02563265805225673 0.19876026897074447 chr7 159138663 4555437 0.028625582960942683 0.29991034090665325 chr8 146364022 8545814 0.05838739523022946 0.2933306316072497 chr9 141213431 2179761 0.015435932577829653 0.1472120808298259 chr10 135534747 3309216 0.02441599717598617 0.17569824214762828 chr11 135006516 3116212 0.02308193776365579 0.1780799172245906 chr12 133851895 2248312 0.01679701284767018 0.14108519717068674 chr13 115169878 1501780 0.013039694285340825 0.12453083724033527 chr14 107349540 1405702 0.01309462527738824 0.12492743064200272 chr15 102531392 1236834 0.012062978721677747 0.1266750484511871 chr16 90354753 1742233 0.01928214003307607 0.1531572023487223 chr17 81195210 1147814 0.014136474306797162 0.13175959795434242 chr18 78077248 2205914 0.028252968137401566 0.21645199402541937 chr19 59128983 1129982 0.019110458909804014 0.16405670162571828 chr20 63025520 1843110 0.029243868198152112 0.18930960037450906 chr21 48129895 1093814 0.022726291008945687 0.16630355379953857 chr22 51304566 724286 0.014117378948298676 0.1296677568541417 chrMT 16571 20656 1.2465149960774848 1.2361588615446335 chrX 155270560 4668620 0.0300676445038905 0.19507573311165213 chrY 59373566 130667 0.002200760520262502 0.05293027737683777