BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081162.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 = 2,348,994 number of mapped reads = 2,114,565 (90.02%) number of supplementary alignments = 19,045 (0.81%) number of secondary alignments = 0 number of mapped bases = 142,546,279 bp number of sequenced bases = 142,492,718 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,799 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.28 >>>>>>> ACTG content number of A's = 40,223,013 bp (28.23%) number of C's = 26,558,218 bp (18.64%) number of T's = 44,386,510 bp (31.15%) number of G's = 31,282,067 bp (21.95%) number of N's = 42,910 bp (0.03%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,172,451 number of insertions = 11,115 mapped reads with insertion percentage = 0.52% number of deletions = 33,173 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.3599X There is a 4.02% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 11355092 0.04555692561343709 0.5686287770725343 chr2 243199373 12639660 0.05197242017560629 0.45077722630807515 chr3 198022430 10024260 0.05062184117223488 0.24885674779021674 chr4 191154276 10171214 0.05320945056965401 0.2641770640103537 chr5 180915260 8577842 0.047413590207923864 0.24286692581851388 chr6 171115067 8807197 0.051469441904844065 0.3143354855707072 chr7 159138663 7213997 0.04533151695512234 0.42654983010924385 chr8 146364022 7015837 0.04793416376601075 0.4985126692433799 chr9 141213431 5427622 0.038435593282908055 0.34528725434859364 chr10 135534747 7349149 0.05422335720300566 0.32960171058791143 chr11 135006516 6885125 0.05099846440004422 0.35086278301173196 chr12 133851895 6260363 0.046770820838957866 0.24618536447337414 chr13 115169878 4408083 0.0382746172571269 0.21690791456744024 chr14 107349540 4576576 0.042632469594187365 0.25584341203443156 chr15 102531392 3590917 0.03502261044110276 0.214693009059862 chr16 90354753 3993412 0.044197032999470434 0.26186463330988025 chr17 81195210 3283227 0.040436215387582596 0.27261503713713575 chr18 78077248 3625450 0.04643414173614316 0.6546486931732568 chr19 59128983 2477673 0.041902851601557226 0.4403862964900464 chr20 63025520 2965424 0.04705116276708229 0.24997242328773572 chr21 48129895 1771803 0.0368129413122551 0.22965437329076313 chr22 51304566 1507437 0.02938212166145212 0.18946496819980785 chrMT 16571 24926 1.504194073984672 1.4460815081485419 chrX 155270560 8277522 0.05331031201278594 0.2839538062777616 chrY 59373566 316471 0.005330166626676929 0.1101859624919976