BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084351.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 = 2,322,856 number of mapped reads = 2,007,440 (86.42%) number of supplementary alignments = 11,533 (0.5%) number of secondary alignments = 0 number of mapped bases = 134,467,841 bp number of sequenced bases = 134,421,793 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,994 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6472 >>>>>>> ACTG content number of A's = 37,143,517 bp (27.63%) number of C's = 26,002,191 bp (19.34%) number of T's = 41,168,155 bp (30.63%) number of G's = 29,943,470 bp (22.28%) number of N's = 164,460 bp (0.12%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,290,286 number of insertions = 9,160 mapped reads with insertion percentage = 0.45% number of deletions = 26,206 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.29X There is a 3.71% of reference with a coverageData >= 1X There is a 0.48% 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 12842731 0.05152537212735771 0.422397714428549 chr2 243199373 15248791 0.06270078253861287 0.37136580127810587 chr3 198022430 8848342 0.044683534082477425 0.24054846473907662 chr4 191154276 6724728 0.03517958447343338 0.21676845583433316 chr5 180915260 6733287 0.03721790522258874 0.21806810213903918 chr6 171115067 6158160 0.03598841474316227 0.23694520520157844 chr7 159138663 7194020 0.04520598492146437 0.38606784981088155 chr8 146364022 6347751 0.04336961305969031 0.27562094637575335 chr9 141213431 4693536 0.03323717840975056 0.2456481495637752 chr10 135534747 9313761 0.06871862165353067 0.3712314777864871 chr11 135006516 7297858 0.05405559832386164 0.3070865782285317 chr12 133851895 6871276 0.05133491759679607 0.2594193920337415 chr13 115169878 3823086 0.033195190152063896 0.2067148162375728 chr14 107349540 3485658 0.03247017173990685 0.21025044262473086 chr15 102531392 2764001 0.02695760728577644 0.19006180574315013 chr16 90354753 2915133 0.03226319483159895 0.21671974668594274 chr17 81195210 3641673 0.044850835412581606 0.25018832423650883 chr18 78077248 3387524 0.043386826338961126 0.3827913921698673 chr19 59128983 2774822 0.04692828895771808 0.3269264657891457 chr20 63025520 2736324 0.04341612730842998 0.2408222580591756 chr21 48129895 1318142 0.027387177969118777 0.1933892765379385 chr22 51304566 1062284 0.020705447542427317 0.16151570535889756 chrMT 16571 9115 0.5500573290688552 0.8050301790205578 chrX 155270560 8011729 0.051598506503744174 0.27504973656888065 chrY 59373566 264109 0.004448259011426061 0.09235920150099043