BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716423.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 = 1,420,880 number of mapped reads = 1,308,277 (92.08%) number of supplementary alignments = 4,513 (0.32%) number of secondary alignments = 0 number of mapped bases = 75,932,561 bp number of sequenced bases = 75,908,020 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,205 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2722 >>>>>>> ACTG content number of A's = 18,503,018 bp (24.38%) number of C's = 14,107,603 bp (18.59%) number of T's = 24,646,393 bp (32.47%) number of G's = 18,649,559 bp (24.57%) number of N's = 1,447 bp (0%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 386,921 number of insertions = 5,242 mapped reads with insertion percentage = 0.4% number of deletions = 15,080 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.1% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.2436X There is a 2.25% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 6392337 0.02564622296367318 0.37951378532316227 chr2 243199373 6020923 0.024757148530970923 0.33764700559951005 chr3 198022430 4339691 0.021915148703103987 0.15920959370531848 chr4 191154276 4695762 0.024565299287367236 0.1902745588482176 chr5 180915260 4291191 0.023719342414785797 0.1647815970343466 chr6 171115067 4069785 0.023783907936055684 0.19237142161959705 chr7 159138663 4367888 0.02744705728739219 0.33824217205073437 chr8 146364022 3992717 0.0272793610440686 0.2958449298343062 chr9 141213431 2530199 0.01791755204928064 0.1753005900431577 chr10 135534747 3379370 0.024933606140128774 0.26500684799447555 chr11 135006516 2732764 0.02024171929597828 0.188911580427643 chr12 133851895 3764719 0.028126004491755608 0.18105968492291152 chr13 115169878 2311561 0.020070881728293574 0.152329302202067 chr14 107349540 2554075 0.023792137348702194 0.1685837489548298 chr15 102531392 2770822 0.02702413325277004 0.17808103884158363 chr16 90354753 2599241 0.02876706441774015 0.19214206080694046 chr17 81195210 3275448 0.04034040924335315 0.22425401380573212 chr18 78077248 1429479 0.018308521837245084 0.2970663879205063 chr19 59128983 1916637 0.03241450981830687 0.31710956125115836 chr20 63025520 2460164 0.03903441018812697 0.21859344435410996 chr21 48129895 980846 0.020379142734468877 0.17940708260791144 chr22 51304566 684755 0.013346862733426106 0.12322987334039698 chrMT 16571 11734 0.7081045199444813 1.0331981938404633 chrX 155270560 4076513 0.026254255797106676 0.18553729068786168 chrY 59373566 283940 0.004782262867620247 0.21815791067736187