BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083616.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 = 1,886,633 number of mapped reads = 1,668,544 (88.44%) number of supplementary alignments = 20,085 (1.06%) number of secondary alignments = 0 number of mapped bases = 110,028,493 bp number of sequenced bases = 109,988,487 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,873 duplication rate = 5.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0129 >>>>>>> ACTG content number of A's = 29,528,976 bp (26.85%) number of C's = 20,470,094 bp (18.61%) number of T's = 34,715,101 bp (31.56%) number of G's = 25,268,647 bp (22.97%) number of N's = 5,669 bp (0.01%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 771,638 number of insertions = 8,025 mapped reads with insertion percentage = 0.48% number of deletions = 24,758 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.13% >>>>>>> Coverage mean coverageData = 0.0355X std coverageData = 0.2857X There is a 2.81% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 12652318 0.050761430199205 0.4396603432871121 chr2 243199373 9624480 0.03957444413312694 0.45068141800624595 chr3 198022430 10634690 0.053704471761103025 0.2907038274264 chr4 191154276 3964864 0.02074169661786692 0.18111338249456246 chr5 180915260 6134820 0.03390990898169673 0.22578054738599454 chr6 171115067 7393154 0.043205745289513285 0.2900313126231046 chr7 159138663 9096652 0.057161797318857704 0.3596820516071731 chr8 146364022 6978474 0.04767888928332401 0.31266534448960964 chr9 141213431 4860352 0.03441848247423434 0.24010215009809818 chr10 135534747 4407663 0.03252053881061216 0.23814969399279265 chr11 135006516 3722563 0.02757320987381083 0.2114937462185061 chr12 133851895 3060798 0.022867050182591737 0.1848902922675748 chr13 115169878 3312896 0.028765299204363142 0.20832621659136277 chr14 107349540 1613816 0.015033282862693217 0.14995129123570775 chr15 102531392 2664521 0.025987367849253425 0.20651754091718028 chr16 90354753 2230221 0.024682940586423827 0.19497604045245104 chr17 81195210 3120954 0.03843766153200417 0.24577452642747188 chr18 78077248 2821933 0.036142833825290564 0.2742842382927675 chr19 59128983 2801829 0.047385036201282205 0.34375680696772315 chr20 63025520 1849896 0.029351538868699536 0.21035867058876268 chr21 48129895 1757193 0.03650938777240216 0.23631808480610905 chr22 51304566 630793 0.012295065511323105 0.13321933732039037 chrMT 16571 3898 0.23523022147124495 0.5632169992796695 chrX 155270560 4502979 0.02900085502364389 0.21319814500499393 chrY 59373566 186736 0.0031451033276323676 0.06752701627074924