BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081932.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 = 2,703,183 number of mapped reads = 2,461,358 (91.05%) number of supplementary alignments = 15,563 (0.58%) number of secondary alignments = 0 number of mapped bases = 169,524,563 bp number of sequenced bases = 169,460,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,862 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0555 >>>>>>> ACTG content number of A's = 48,512,953 bp (28.63%) number of C's = 31,839,365 bp (18.79%) number of T's = 52,731,359 bp (31.12%) number of G's = 36,355,167 bp (21.45%) number of N's = 21,618 bp (0.01%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,365,154 number of insertions = 13,386 mapped reads with insertion percentage = 0.54% number of deletions = 35,853 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 0.0548X std coverageData = 0.6124X There is a 4.71% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15822491 0.06348024705623502 1.1656618263706808 chr2 243199373 15023471 0.0617742998868669 0.7909157885453242 chr3 198022430 10570912 0.053382397135516416 0.2630209939349449 chr4 191154276 8915246 0.046639009006526226 0.28913029395481354 chr5 180915260 8622261 0.04765911399624333 0.24921362184025705 chr6 171115067 14600332 0.08532464297840002 0.4963068766999705 chr7 159138663 11371767 0.07145822885290924 0.9236333980320077 chr8 146364022 9759484 0.06667952866176362 0.7966415051745876 chr9 141213431 7898856 0.0559355859004658 0.6356582450310743 chr10 135534747 7148397 0.05274217245559915 0.6675993541677846 chr11 135006516 7511195 0.05563579612705508 0.42094005769933585 chr12 133851895 7214094 0.05389609164666664 0.27823744576763065 chr13 115169878 4616191 0.04008158279025007 0.220680175606345 chr14 107349540 4273716 0.03981121856693564 0.27464747475271467 chr15 102531392 3905255 0.03808838370203732 0.21936473870908205 chr16 90354753 3549809 0.03928746282998527 0.30922773901214595 chr17 81195210 4362939 0.05373394563546298 0.31646527323467627 chr18 78077248 4943146 0.06331096608323081 1.114408381933401 chr19 59128983 3538922 0.05985088564773725 0.8488873841903788 chr20 63025520 3782030 0.0600079142544163 0.2861965842721252 chr21 48129895 1822761 0.03787170115372161 0.2779792239093382 chr22 51304566 1335637 0.026033491833845745 0.17673576030738536 chrMT 16571 41866 2.5264618912558086 2.058441948256215 chrX 155270560 8481306 0.05462275656119228 0.3390439706927541 chrY 59373566 412479 0.0069471825222692535 0.2037683591192925