BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081730.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 = 2,678,115 number of mapped reads = 2,445,312 (91.31%) number of supplementary alignments = 16,860 (0.63%) number of secondary alignments = 0 number of mapped bases = 164,612,246 bp number of sequenced bases = 164,556,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,271 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9115 >>>>>>> ACTG content number of A's = 45,478,483 bp (27.64%) number of C's = 31,632,053 bp (19.22%) number of T's = 50,529,929 bp (30.71%) number of G's = 36,913,968 bp (22.43%) number of N's = 1,785 bp (0%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,301,144 number of insertions = 11,201 mapped reads with insertion percentage = 0.45% number of deletions = 31,505 mapped reads with deletion percentage = 1.27% homopolymer indels = 47.08% >>>>>>> Coverage mean coverageData = 0.0532X std coverageData = 0.3541X There is a 4.45% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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% 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 13254408 0.05317703100125877 0.5238701602349086 chr2 243199373 13792337 0.05671205821735404 0.4450470542595419 chr3 198022430 11754130 0.05935756873602652 0.28241159029963814 chr4 191154276 10708113 0.056018171416683346 0.28925204515811503 chr5 180915260 11010365 0.060859238739728205 0.2851942325186468 chr6 171115067 9724116 0.056827935555201575 0.30624660564688716 chr7 159138663 8585375 0.05394902054694276 0.40658114595952966 chr8 146364022 8758593 0.05984116096509018 0.4185492681268725 chr9 141213431 6419033 0.04545624983787838 0.3418055099579748 chr10 135534747 7239405 0.053413646022447664 0.3901685146467961 chr11 135006516 6994775 0.0518106474208993 0.3149975240164515 chr12 133851895 6885944 0.05144450140209072 0.2646175456392995 chr13 115169878 5447520 0.047299867765771185 0.2517341821099385 chr14 107349540 4990950 0.046492514080637884 0.26232386801123597 chr15 102531392 4611852 0.04497990235029677 0.2487344947535115 chr16 90354753 4717268 0.05220829943500593 0.291428964507401 chr17 81195210 4409055 0.05430191017425782 0.2839106404026137 chr18 78077248 4503541 0.05768058064751463 0.5447700661064295 chr19 59128983 3231377 0.05464962926894921 0.42640231010286567 chr20 63025520 3421940 0.054294514349108106 0.27610278088738965 chr21 48129895 2157097 0.044818236150317804 0.26171197468753654 chr22 51304566 1645489 0.03207295428636898 0.20541175293067498 chrMT 16571 1100 0.06638102709552833 0.25985852700650014 chrX 155270560 9915355 0.06385856404459415 0.3197737190532949 chrY 59373566 433108 0.0072946267030685 0.16370694395306779