BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008754.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 8,276,360 number of mapped reads = 1,634,103 (19.74%) number of supplementary alignments = 5,647 (0.07%) number of secondary alignments = 0 number of mapped bases = 100,454,365 bp number of sequenced bases = 100,404,858 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,119 duplication rate = 2.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4102 >>>>>>> ACTG content number of A's = 27,645,423 bp (27.53%) number of C's = 18,475,579 bp (18.4%) number of T's = 29,410,872 bp (29.29%) number of G's = 24,844,730 bp (24.74%) number of N's = 28,254 bp (0.03%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 1,021,121 number of insertions = 7,331 mapped reads with insertion percentage = 0.44% number of deletions = 31,718 mapped reads with deletion percentage = 1.92% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 0.0324X std coverageData = 0.2548X There is a 2.81% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.06% 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% 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 8788266 0.03525875267528421 0.36618581286345747 chr2 243199373 8867223 0.03646071488843847 0.3114595017707998 chr3 198022430 8700286 0.043935861205218016 0.24346082320033888 chr4 191154276 5136387 0.026870374586859883 0.19280799730513626 chr5 180915260 5154157 0.028489343574444742 0.19305463944447068 chr6 171115067 5203230 0.030407784020562025 0.21635061501098288 chr7 159138663 5631645 0.035388289016855694 0.310435997590865 chr8 146364022 7641958 0.052211997836462846 0.29946630276235 chr9 141213431 2955600 0.020930020459597784 0.21185744214572655 chr10 135534747 5514467 0.040686739910319826 0.31001778390556134 chr11 135006516 3648464 0.027024354883730204 0.22860760123646268 chr12 133851895 4187624 0.03128550402667067 0.20414856619723715 chr13 115169878 2556804 0.02220028400134278 0.17468507831998045 chr14 107349540 3609251 0.03362148547632342 0.21125932217612892 chr15 102531392 2926590 0.02854335577537073 0.2034766024072124 chr16 90354753 2511594 0.027797032437242124 0.2154860184880623 chr17 81195210 3025753 0.037265166257960294 0.24423843495991365 chr18 78077248 1824087 0.023362593415177747 0.3263880517138977 chr19 59128983 2131340 0.03604560558736483 0.2781703988219329 chr20 63025520 2398070 0.038049190232781895 0.2261435023037547 chr21 48129895 1127804 0.02343250489119081 0.18616499430656777 chr22 51304566 1306437 0.025464341711807875 0.18503361973796772 chrMT 16571 42051 2.5376259730855106 2.563387721638962 chrX 155270560 5302536 0.03415029867864198 0.22456518272670314 chrY 59373566 262741 0.004425218454960243 0.09985454324388603