BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080682.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 = 1,334,949 number of mapped reads = 1,234,625 (92.48%) number of supplementary alignments = 11,295 (0.85%) number of secondary alignments = 0 number of mapped bases = 82,816,969 bp number of sequenced bases = 82,785,913 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,158 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4133 >>>>>>> ACTG content number of A's = 22,995,004 bp (27.78%) number of C's = 15,034,626 bp (18.16%) number of T's = 26,519,405 bp (32.03%) number of G's = 18,233,391 bp (22.02%) number of N's = 3,487 bp (0%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 561,289 number of insertions = 6,145 mapped reads with insertion percentage = 0.49% number of deletions = 19,190 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.9% >>>>>>> Coverage mean coverageData = 0.0268X std coverageData = 0.2114X There is a 2.37% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 10103001 0.040533503826255264 0.27618842933748045 chr2 243199373 5491404 0.022579844397871866 0.2694044881588521 chr3 198022430 5113081 0.025820716370362692 0.17604894247059324 chr4 191154276 4083862 0.0213642199664945 0.16305179312754478 chr5 180915260 3799798 0.021003192323300977 0.15903499218418507 chr6 171115067 5090200 0.029747234356633248 0.2122431399838128 chr7 159138663 5173679 0.03251050940399066 0.32814335787348964 chr8 146364022 10006730 0.06836878259603989 0.3185236134058997 chr9 141213431 2618139 0.01854029734607893 0.1713278868907896 chr10 135534747 3836442 0.02830596643973519 0.19337083690895204 chr11 135006516 3547133 0.02627379111094164 0.18760508241754198 chr12 133851895 2576148 0.01924625721585787 0.15345718570410388 chr13 115169878 1613636 0.014010920459601424 0.13069660680003484 chr14 107349540 1628408 0.01516921264869882 0.13722870795276354 chr15 102531392 1508943 0.014716887877617033 0.14096932520014094 chr16 90354753 1889580 0.020912900951652207 0.16020660156552383 chr17 81195210 1257021 0.015481467441244378 0.13775475502033846 chr18 78077248 2570430 0.03292162654093546 0.24225224485856384 chr19 59128983 1222177 0.020669677339114727 0.18132029731621183 chr20 63025520 2021170 0.032069072972345174 0.1987496443105973 chr21 48129895 1204491 0.025025838930253223 0.17526989386435834 chr22 51304566 774798 0.01510193069365405 0.1343093937961409 chrMT 16571 12658 0.7638645827047251 1.0357070172030387 chrX 155270560 5503770 0.03544632028119175 0.21302204443169082 chrY 59373566 170270 0.002867774524440725 0.061828559919515844