BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238081.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 = 1,913,795 number of mapped reads = 1,220,055 (63.75%) number of supplementary alignments = 12,110 (0.63%) number of secondary alignments = 0 number of mapped bases = 74,015,104 bp number of sequenced bases = 73,979,083 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,185 duplication rate = 12.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0835 >>>>>>> ACTG content number of A's = 19,598,816 bp (26.49%) number of C's = 12,763,497 bp (17.25%) number of T's = 24,207,177 bp (32.72%) number of G's = 17,406,128 bp (23.53%) number of N's = 3,465 bp (0%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 561,100 number of insertions = 5,687 mapped reads with insertion percentage = 0.46% number of deletions = 22,705 mapped reads with deletion percentage = 1.84% homopolymer indels = 45.88% >>>>>>> Coverage mean coverageData = 0.0239X std coverageData = 0.3112X There is a 1.51% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% 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 8281430 0.03322531340854713 0.5431021521182745 chr2 243199373 5414338 0.022262960357220987 0.374672108792876 chr3 198022430 6289283 0.03176045764108642 0.27475354131512064 chr4 191154276 5548823 0.029027982612327228 0.2592213056366214 chr5 180915260 3424351 0.018927927914980748 0.20183893916219015 chr6 171115067 3581945 0.020932960859606827 0.25001101927049835 chr7 159138663 3187919 0.020032334945531118 0.2585031829746573 chr8 146364022 3775164 0.02579297800384305 0.4045038480096432 chr9 141213431 3706067 0.026244437046501617 0.27554932004705224 chr10 135534747 3948014 0.029129164936575268 0.3226763081410383 chr11 135006516 3455714 0.02559664601670041 0.28433363827596897 chr12 133851895 2943012 0.02198707758302563 0.23386996125799012 chr13 115169878 2456379 0.02132831120998496 0.22762528808178836 chr14 107349540 1675055 0.015603746415680962 0.1921346007319034 chr15 102531392 2013218 0.019635137695194853 0.20992052512710835 chr16 90354753 1710942 0.01893582731613466 0.20889927359718233 chr17 81195210 2345856 0.028891556533938392 0.26295056033731656 chr18 78077248 1985748 0.02543311977389367 0.5114253270252833 chr19 59128983 1327673 0.02245384467377022 0.3580447693674859 chr20 63025520 1688674 0.026793495714117075 0.24315474024307082 chr21 48129895 806488 0.016756487833601133 0.19418466296196232 chr22 51304566 866742 0.016894051886142063 0.1908123658523209 chrMT 16571 55138 3.327379156357492 3.124924350392806 chrX 155270560 3198027 0.0205964801054366 0.2259381356421173 chrY 59373566 329104 0.0055429380812329855 0.12146649351333964