BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081161.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 = 2,336,075 number of mapped reads = 2,111,037 (90.37%) number of supplementary alignments = 24,282 (1.04%) number of secondary alignments = 0 number of mapped bases = 143,127,594 bp number of sequenced bases = 143,074,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,216 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0869 >>>>>>> ACTG content number of A's = 40,764,115 bp (28.49%) number of C's = 26,828,531 bp (18.75%) number of T's = 44,569,890 bp (31.15%) number of G's = 30,868,964 bp (21.58%) number of N's = 43,406 bp (0.03%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,165,863 number of insertions = 10,888 mapped reads with insertion percentage = 0.51% number of deletions = 32,243 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.01% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.3662X There is a 3.97% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 11426986 0.045845366218766614 0.6477191882019405 chr2 243199373 11339982 0.04662833567420423 0.41445830185539845 chr3 198022430 9067312 0.045789317907067396 0.2401211903341417 chr4 191154276 9213443 0.048198989804444654 0.25567830414246256 chr5 180915260 9389614 0.05190061910753134 0.2581364315334566 chr6 171115067 9329622 0.05452250443848992 0.3454070524614876 chr7 159138663 7818903 0.049132642266826135 0.4391526467146391 chr8 146364022 7243813 0.04949175966208417 0.4681958014665199 chr9 141213431 6143891 0.043507837437927556 0.3378340694877848 chr10 135534747 6832217 0.050409338942433705 0.3185629068156958 chr11 135006516 6607159 0.04893955636926443 0.3608730740344479 chr12 133851895 6069088 0.04534181604227568 0.2427571698481922 chr13 115169878 4729646 0.04106669280313035 0.22787294490675922 chr14 107349540 4733592 0.044095130729018495 0.25650411985578975 chr15 102531392 4370324 0.0426242530677824 0.2344014706915632 chr16 90354753 3320791 0.036752809229637314 0.24210047104111151 chr17 81195210 3402592 0.041906314424212956 0.2689725819085517 chr18 78077248 3833031 0.049092803578322845 0.5992639224399594 chr19 59128983 2636141 0.0445828909318464 0.4627887055498086 chr20 63025520 3114168 0.04941122262854793 0.25605033912696606 chr21 48129895 2025820 0.04209067981552837 0.24233062085077914 chr22 51304566 1407729 0.027438668909118148 0.18434155064074706 chrMT 16571 24248 1.4632792227385192 1.4083609944185769 chrX 155270560 8708822 0.05608804399237048 0.300496831239365 chrY 59373566 338660 0.005703885126252986 0.11512218013270763