BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708532.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,243,614 number of mapped reads = 2,058,043 (91.73%) number of supplementary alignments = 103 (0%) number of secondary alignments = 0 number of mapped bases = 104,036,242 bp number of sequenced bases = 104,025,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,770 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.304 >>>>>>> ACTG content number of A's = 30,921,091 bp (29.72%) number of C's = 20,895,249 bp (20.09%) number of T's = 31,348,156 bp (30.14%) number of G's = 20,859,174 bp (20.05%) number of N's = 1,514 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 480,649 number of insertions = 4,860 mapped reads with insertion percentage = 0.24% number of deletions = 6,586 mapped reads with deletion percentage = 0.32% homopolymer indels = 43.47% >>>>>>> Coverage mean coverageData = 0.0336X std coverageData = 0.3172X There is a 3.14% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.01% 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 8551517 0.034308909505184344 0.6533646642217358 chr2 243199373 8912110 0.03664528362085868 0.2499443993208354 chr3 198022430 7060742 0.035656273887761096 0.2054701390640455 chr4 191154276 7072598 0.036999423439525884 0.22294351421815872 chr5 180915260 6486374 0.035853106034283676 0.19687315071556438 chr6 171115067 6130347 0.03582587499439777 0.21521792637889683 chr7 159138663 5819595 0.03656933450546836 0.30952446879363804 chr8 146364022 5283447 0.03609798998281149 0.3458006632106339 chr9 141213431 4376778 0.030994063163864348 0.19996439871800895 chr10 135534747 5343799 0.03942752038338921 0.5806222903798219 chr11 135006516 4806781 0.03560406669556601 0.23112993282992925 chr12 133851895 4744469 0.03544566178909906 0.19615038655234648 chr13 115169878 3424636 0.029735518170818934 0.17715904323564338 chr14 107349540 3208785 0.029890999067159488 0.18100246534915201 chr15 102531392 2946896 0.028741402437996746 0.1741057109934408 chr16 90354753 3189424 0.03529890674373267 0.2929294481807697 chr17 81195210 2793484 0.03440454184427875 0.21244510038916548 chr18 78077248 2772847 0.03551414875688241 0.3021459182399852 chr19 59128983 2088858 0.03532714235927244 0.49957475086537123 chr20 63025520 2125970 0.03373189146237905 0.19319119205277457 chr21 48129895 1437168 0.029860193960531183 0.22037084146898583 chr22 51304566 1217666 0.02373406686648514 0.18837188483700754 chrMT 16571 214896 12.968197453382414 4.98228512070146 chrX 155270560 3084702 0.01986662507045766 0.1593910492871719 chrY 59373566 942353 0.015871591745053683 0.24069432805796048