BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238613.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 = 3,619,033 number of mapped reads = 2,395,143 (66.18%) number of supplementary alignments = 18,003 (0.5%) number of secondary alignments = 0 number of mapped bases = 147,268,472 bp number of sequenced bases = 147,208,428 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 604,974 duplication rate = 18.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4262 >>>>>>> ACTG content number of A's = 36,387,341 bp (24.72%) number of C's = 26,367,990 bp (17.91%) number of T's = 48,676,442 bp (33.07%) number of G's = 35,769,287 bp (24.3%) number of N's = 7,368 bp (0.01%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 794,384 number of insertions = 9,619 mapped reads with insertion percentage = 0.4% number of deletions = 34,713 mapped reads with deletion percentage = 1.44% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.612X There is a 2.39% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 10947330 0.043920973821766324 0.6303836179277971 chr2 243199373 12372455 0.05087371257326391 1.2982171303905872 chr3 198022430 9166056 0.04628796848922619 0.39390405409597135 chr4 191154276 10718368 0.05607181918336998 0.43565679796851353 chr5 180915260 9428767 0.05211703534571931 0.4140045158709925 chr6 171115067 7046053 0.04117727984760103 0.5442406580773617 chr7 159138663 7925165 0.04980037440681527 0.6260303244566128 chr8 146364022 7033364 0.048053913139938176 0.5065793498497351 chr9 141213431 5399785 0.038238466141368666 0.40855434646615535 chr10 135534747 8191353 0.060437291405428306 0.529029255052757 chr11 135006516 5573329 0.041281925977558004 0.40252830507107296 chr12 133851895 10616766 0.07931726330807644 0.5282803434196628 chr13 115169878 4133626 0.035891554908133186 0.43369243328635265 chr14 107349540 3171671 0.029545268661607678 0.3188941533326672 chr15 102531392 4397366 0.042887996683006115 0.4586244032147859 chr16 90354753 4213395 0.04663169186019467 0.424202427011639 chr17 81195210 2666882 0.03284531193404143 0.3323025994138226 chr18 78077248 3274111 0.04193425208839328 1.2505317753504608 chr19 59128983 3932006 0.06649879298617398 0.5730394807580512 chr20 63025520 2221949 0.03525475077397219 0.3460159826947656 chr21 48129895 2028234 0.042140835752914066 0.3773952981784152 chr22 51304566 1113455 0.021702844148413614 0.2570437151500147 chrMT 16571 40098 2.4197694767968136 2.8430944802202567 chrX 155270560 11271851 0.07259490144171567 0.4959523056697566 chrY 59373566 385037 0.0064849903069658975 0.24308155154470668