BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080552.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 = 2,750,971 number of mapped reads = 2,267,046 (82.41%) number of supplementary alignments = 19,460 (0.71%) number of secondary alignments = 0 number of mapped bases = 152,020,038 bp number of sequenced bases = 151,961,680 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,988 duplication rate = 4.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6942 >>>>>>> ACTG content number of A's = 42,015,217 bp (27.65%) number of C's = 27,263,325 bp (17.94%) number of T's = 49,427,355 bp (32.53%) number of G's = 33,128,433 bp (21.8%) number of N's = 127,350 bp (0.08%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,355,446 number of insertions = 12,341 mapped reads with insertion percentage = 0.54% number of deletions = 35,530 mapped reads with deletion percentage = 1.55% homopolymer indels = 49.62% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 0.3228X There is a 3.93% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.16% 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 12915162 0.051815967190709626 0.44584030915182804 chr2 243199373 12979511 0.05336983742963844 0.3283081773800358 chr3 198022430 11146491 0.056289032510105044 0.28659565409649135 chr4 191154276 10089461 0.05278176984123546 0.28068749051220543 chr5 180915260 9692240 0.05357336910109186 0.27981210765814124 chr6 171115067 8969193 0.052416149888191904 0.3194505155981556 chr7 159138663 8032412 0.05047429611746832 0.49008853227325905 chr8 146364022 7550987 0.05159045848029511 0.4103749768330808 chr9 141213431 5871201 0.04157678882541987 0.27452708088732497 chr10 135534747 6379496 0.047069081111724066 0.2880656526905009 chr11 135006516 6900017 0.051108770187062676 0.28809029851703455 chr12 133851895 6927278 0.05175330539773083 0.27367862819863814 chr13 115169878 4926642 0.04277717477481395 0.25059942020240544 chr14 107349540 4746105 0.044211693874049204 0.2595071615679744 chr15 102531392 4122281 0.04020506227009968 0.24109058226405794 chr16 90354753 3928539 0.043479051954245285 0.2629378285147114 chr17 81195210 3867452 0.047631529002757675 0.2717856970692165 chr18 78077248 3850271 0.049313610541191204 0.3870774545428887 chr19 59128983 2772687 0.046892181453552145 0.3559996423263924 chr20 63025520 2742146 0.04350850258752328 0.2549722586382714 chr21 48129895 1978824 0.041114238873781045 0.24995173651401764 chr22 51304566 1657745 0.0323118414060846 0.21605047526622514 chrMT 16571 78455 4.734475891617887 4.547927676615122 chrX 155270560 9576109 0.06167369397006103 0.31137600922979936 chrY 59373566 319333 0.005378369896125154 0.10375038254543843