BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230389.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 = 2,330,595 number of mapped reads = 1,314,375 (56.4%) number of supplementary alignments = 7,198 (0.31%) number of secondary alignments = 0 number of mapped bases = 83,715,046 bp number of sequenced bases = 83,670,828 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,287 duplication rate = 6.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1712 >>>>>>> ACTG content number of A's = 22,083,156 bp (26.39%) number of C's = 14,382,843 bp (17.19%) number of T's = 28,139,563 bp (33.63%) number of G's = 18,929,786 bp (22.62%) number of N's = 135,480 bp (0.16%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 984,280 number of insertions = 7,243 mapped reads with insertion percentage = 0.55% number of deletions = 27,725 mapped reads with deletion percentage = 2.08% homopolymer indels = 49.29% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2741X There is a 1.95% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 8338711 0.03345512627629522 0.43139408048303063 chr2 243199373 7354152 0.030239189802516473 0.2891994035646478 chr3 198022430 5281485 0.026671145283895366 0.21809635621067872 chr4 191154276 6077435 0.031793351041752266 0.24661473583566504 chr5 180915260 5322448 0.029419563612267975 0.2323038169414298 chr6 171115067 4504574 0.026324823868373905 0.24768328924741712 chr7 159138663 4305396 0.0270543683026921 0.3093473613159881 chr8 146364022 5097372 0.03482667345667776 0.35368115735812006 chr9 141213431 3550430 0.02514229684002225 0.26324511042291837 chr10 135534747 3640322 0.026858957430303834 0.2566909566563106 chr11 135006516 3706563 0.027454697075510043 0.2658808405369713 chr12 133851895 4034354 0.03014043245334704 0.23593437890326896 chr13 115169878 2246664 0.019507392375634886 0.18755734532818286 chr14 107349540 2225157 0.020728146576128783 0.20138990610163066 chr15 102531392 2039100 0.019887567702192126 0.1898155749712874 chr16 90354753 2084318 0.023068161118209245 0.21050368949323747 chr17 81195210 2054898 0.025308118545416657 0.22692964194247361 chr18 78077248 1698902 0.021759245407829947 0.3878417094931491 chr19 59128983 1362812 0.023048121764583707 0.29985862746948383 chr20 63025520 1638534 0.025997944959438652 0.22008496112016845 chr21 48129895 1079825 0.02243564005281956 0.2117826410436263 chr22 51304566 842500 0.016421540336195417 0.16650608787377602 chrMT 16571 97070 5.857823909239032 4.7731133611659216 chrX 155270560 4927592 0.03173552024285866 0.2509322341122738 chrY 59373566 204432 0.003443148420628803 0.08574503820240023