BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013172.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,081,393 number of mapped reads = 1,843,595 (88.58%) number of supplementary alignments = 15,703 (0.75%) number of secondary alignments = 0 number of mapped bases = 121,365,271 bp number of sequenced bases = 121,304,774 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,169 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9399 >>>>>>> ACTG content number of A's = 33,276,383 bp (27.43%) number of C's = 22,996,848 bp (18.96%) number of T's = 37,713,315 bp (31.09%) number of G's = 27,289,341 bp (22.5%) number of N's = 28,887 bp (0.02%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 998,422 number of insertions = 8,123 mapped reads with insertion percentage = 0.44% number of deletions = 34,841 mapped reads with deletion percentage = 1.87% homopolymer indels = 44.67% >>>>>>> Coverage mean coverageData = 0.0392X std coverageData = 0.3429X There is a 3.27% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% 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 8942156 0.035876163373731375 0.5830427337527956 chr2 243199373 12340293 0.05074146716652925 0.39942651619475283 chr3 198022430 7585030 0.038303893149882064 0.22617728637266 chr4 191154276 7731703 0.04044744989120724 0.2392293729228062 chr5 180915260 6505356 0.03595802808452974 0.21970173111038377 chr6 171115067 6541854 0.038230730435911874 0.27401671162172314 chr7 159138663 7580166 0.047632460001250605 0.5447157101925394 chr8 146364022 6764921 0.04621983536363875 0.3503176258511198 chr9 141213431 4385798 0.03105793810788437 0.26743547183558625 chr10 135534747 5727287 0.0422569645553697 0.37058928925378615 chr11 135006516 5049383 0.03740103181390149 0.26213534193698795 chr12 133851895 6011459 0.04491127301559683 0.24721654326775636 chr13 115169878 3058091 0.026552871750024777 0.1896240860110249 chr14 107349540 3958786 0.03687753110073876 0.23728886096462665 chr15 102531392 3370151 0.03286945523962066 0.20940351483487588 chr16 90354753 4018973 0.044479929019340024 0.26594190785818655 chr17 81195210 3159312 0.03891007856251619 0.2472429350679017 chr18 78077248 3073582 0.039365911052602676 0.47887274670233543 chr19 59128983 2488257 0.042081850114012616 0.46232269749907323 chr20 63025520 2755163 0.043715037971919946 0.2471481931865914 chr21 48129895 2054960 0.042696124726638196 0.2500982735920897 chr22 51304566 1237248 0.02411574829421615 0.1778873605095465 chrMT 16571 372967 22.507211393398105 12.163754217609917 chrX 155270560 6389345 0.0411497517623431 0.2525622101766743 chrY 59373566 263030 0.004430085940938767 0.09800582660773005