BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548999.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,603,071 number of mapped reads = 7,422,075 (86.27%) number of secondary alignments = 0 number of mapped bases = 294,732,578 bp number of sequenced bases = 294,700,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 717,939 duplication rate = 8.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8792 >>>>>>> ACTG content number of A's = 89,140,615 bp (30.25%) number of C's = 57,929,102 bp (19.66%) number of T's = 89,226,982 bp (30.28%) number of G's = 58,401,149 bp (19.82%) number of N's = 2,899 bp (0%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 831,833 number of insertions = 8,509 mapped reads with insertion percentage = 0.11% number of deletions = 24,797 mapped reads with deletion percentage = 0.33% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.0952X std coverageData = 0.8514X There is a 6.48% of reference with a coverageData >= 1X There is a 1.95% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23559639 0.09452188686823773 1.1753970955739697 chr2 243199373 25852298 0.1063008414910675 0.5624965174324262 chr3 198022430 20977473 0.10593483273586735 0.4471026376294925 chr4 191154276 20728620 0.10843921691817138 0.49071055064010766 chr5 180915260 19148410 0.10584187315099898 0.4498685976842826 chr6 171115067 18042477 0.10544060973894251 0.4956293463108602 chr7 159138663 16485873 0.1035943917663805 0.8199528743459535 chr8 146364022 15792113 0.10789613994072943 2.7626988883997528 chr9 141213431 12542022 0.0888160701937764 0.5100034324179632 chr10 135534747 13857209 0.10224100687626621 0.6059582025920849 chr11 135006516 13726513 0.10167296665888334 0.5400741533812284 chr12 133851895 13665171 0.10209172608277231 0.4528119264580049 chr13 115169878 10141608 0.0880578166454253 0.40506785069559265 chr14 107349540 9239725 0.08607139816342017 0.454689455808961 chr15 102531392 8352473 0.08146259245168543 0.3845639535470723 chr16 90354753 7592693 0.08403202651663494 0.4242664326150113 chr17 81195210 6926967 0.08531250796691085 0.4162937395664641 chr18 78077248 8171254 0.10465601963839709 0.9905914754807067 chr19 59128983 4643881 0.07853815107897255 0.87217263288797 chr20 63025520 5840467 0.09266828738580817 0.43666987563183396 chr21 48129895 3911327 0.08126606135334391 0.4557811956367349 chr22 51304566 2813150 0.05483235156886426 0.3413836525124855 chrMT 16571 6448 0.38911351155633334 0.790192282110006 chrX 155270560 9977426 0.06425832430822688 0.4176237737873813 chrY 59373566 2737341 0.04610369874027779 0.5342825377152607