BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084849.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 = 2,774,113 number of mapped reads = 2,486,554 (89.63%) number of supplementary alignments = 20,712 (0.75%) number of secondary alignments = 0 number of mapped bases = 172,566,190 bp number of sequenced bases = 172,500,434 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,863 duplication rate = 4.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.3934 >>>>>>> ACTG content number of A's = 50,407,304 bp (29.22%) number of C's = 31,358,477 bp (18.18%) number of T's = 55,762,257 bp (32.33%) number of G's = 34,945,290 bp (20.26%) number of N's = 27,106 bp (0.02%) GC percentage = 38.44% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,398,638 number of insertions = 13,610 mapped reads with insertion percentage = 0.54% number of deletions = 37,255 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.58% >>>>>>> Coverage mean coverageData = 0.0557X std coverageData = 0.4539X There is a 4.36% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13392618 0.05373153313026249 0.5316001977747915 chr2 243199373 15380916 0.06324406107741075 0.3935307297758735 chr3 198022430 12453551 0.06288959791070133 0.3055650706041142 chr4 191154276 11914750 0.06233054394242272 0.30889376255895 chr5 180915260 11490240 0.06351172366554375 0.3069603133847102 chr6 171115067 10085149 0.05893781989402488 0.2996842507498191 chr7 159138663 9400032 0.059068185083344577 0.4248719186259814 chr8 146364022 9301013 0.06354712635595652 1.3054356231194533 chr9 141213431 6626102 0.04692260469190073 0.3539380083437993 chr10 135534747 7961032 0.058737941201159286 0.3816859848092879 chr11 135006516 7917334 0.0586440879638728 0.34621293137475745 chr12 133851895 7919016 0.059162524370685976 0.29752181352722373 chr13 115169878 5929255 0.05148268890238818 0.27703409221067254 chr14 107349540 5164389 0.048108161432270695 0.2798706177443959 chr15 102531392 4807982 0.04689277992051449 0.26224320985925736 chr16 90354753 4205512 0.04654444686490372 0.2890840669719212 chr17 81195210 3776485 0.046511179661952964 0.27337739619046564 chr18 78077248 4520731 0.05790074721895936 0.704333468163288 chr19 59128983 2596665 0.04391526571664525 0.40436078474496684 chr20 63025520 3163460 0.05019331851605508 0.28028123193191473 chr21 48129895 2317052 0.04814163837257488 0.27622282820744526 chr22 51304566 1657052 0.03229833383640746 0.21451618440128825 chrMT 16571 155811 9.402631102528513 5.5504421327115745 chrX 155270560 10051049 0.06473248373677534 0.3244376353669856 chrY 59373566 378994 0.00638321100672983 0.13494909784298403