BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716708.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,324,754 number of mapped reads = 2,163,290 (93.05%) number of supplementary alignments = 60,226 (2.59%) number of secondary alignments = 0 number of mapped bases = 165,959,585 bp number of sequenced bases = 165,892,216 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 125,706 duplication rate = 4.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3639 >>>>>>> ACTG content number of A's = 40,809,510 bp (24.6%) number of C's = 32,925,102 bp (19.85%) number of T's = 50,621,903 bp (30.51%) number of G's = 41,528,953 bp (25.03%) number of N's = 6,748 bp (0%) GC percentage = 44.88% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,140,938 number of insertions = 15,981 mapped reads with insertion percentage = 0.73% number of deletions = 32,349 mapped reads with deletion percentage = 1.47% homopolymer indels = 38.37% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.452X There is a 4.28% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18654160 0.07484097702609134 0.8705811247890306 chr2 243199373 11457486 0.04711149481458573 0.4517096069624727 chr3 198022430 10979286 0.055444658466215165 0.29028195147434743 chr4 191154276 8215546 0.04297861482313898 0.40776747551923564 chr5 180915260 10371719 0.057329155097253816 0.29403505602831453 chr6 171115067 10516281 0.061457364242507063 0.32145359747937496 chr7 159138663 10883507 0.06839008695203126 0.6244920733157374 chr8 146364022 10086991 0.06891714823196099 0.45792569743490164 chr9 141213431 5063532 0.03585729745494251 0.30093269256567656 chr10 135534747 9387485 0.0692625707266049 0.6815217718566894 chr11 135006516 5013453 0.03713489651121728 0.3294481766982012 chr12 133851895 5923798 0.044256362601366235 0.25473904389041313 chr13 115169878 3062877 0.026594427754798873 0.19011528991083892 chr14 107349540 3387137 0.031552412800278415 0.2285660449528021 chr15 102531392 3580712 0.03492307994804167 0.22247811917474936 chr16 90354753 5195465 0.0575007382290116 0.3242543944986613 chr17 81195210 3161861 0.03894147204003783 0.2649516431825726 chr18 78077248 4923273 0.06305643610799397 0.48735267713071345 chr19 59128983 4420964 0.07476813866391038 0.6264249037195121 chr20 63025520 3685438 0.058475328723983554 0.32582898241330077 chr21 48129895 3007464 0.06248640268174281 0.4030423411513314 chr22 51304566 3626049 0.07067692571456505 0.3456642430509751 chrMT 16571 147893 8.924808400217247 6.61852317564737 chrX 155270560 10616075 0.06837146075856235 0.3342476551424379 chrY 59373566 591133 0.009956164667623299 0.36401666033509017