BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174076.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,046,386 number of mapped reads = 2,976,091 (97.69%) number of supplementary alignments = 281,713 (9.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,489,246 number of mapped paired reads (second in pair) = 1,486,845 number of mapped paired reads (both in pair) = 2,931,166 number of mapped paired reads (singletons) = 44,925 number of mapped bases = 353,302,849 bp number of sequenced bases = 353,112,559 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,297,632 duplication rate = 65.11% >>>>>>> Insert size mean insert size = 821,584.3672 std insert size = 8,476,970.0669 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.8007 >>>>>>> ACTG content number of A's = 106,728,120 bp (30.22%) number of C's = 68,982,441 bp (19.54%) number of T's = 106,210,284 bp (30.08%) number of G's = 71,187,034 bp (20.16%) number of N's = 4,680 bp (0%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 3,545,403 number of insertions = 36,869 mapped reads with insertion percentage = 1.2% number of deletions = 77,491 mapped reads with deletion percentage = 2.54% homopolymer indels = 42.66% >>>>>>> Coverage mean coverageData = 0.1141X std coverageData = 1.7436X There is a 2.42% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 1.47% of reference with a coverageData >= 3X There is a 1.2% of reference with a coverageData >= 4X There is a 0.91% of reference with a coverageData >= 5X There is a 0.74% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 30484194 0.12230338234543456 1.480269730069727 chr2 243199373 37236306 0.15311020559251196 4.748966706312881 chr3 198022430 23963576 0.12101445275669023 1.002998670327309 chr4 191154276 21970122 0.11493398138789215 1.0823661756214917 chr5 180915260 26629539 0.14719343741373725 1.1174120114440664 chr6 171115067 21050744 0.12302098447005838 1.0312626299270153 chr7 159138663 23208780 0.14583998358714376 1.6072529986862214 chr8 146364022 15774158 0.10777346635090419 1.0559424386594167 chr9 141213431 14300722 0.10127026798180408 1.0102294548739854 chr10 135534747 14575472 0.10754048185149157 1.8405957120308292 chr11 135006516 18372022 0.13608248360397657 1.0703138841674023 chr12 133851895 12514009 0.09349145934766183 0.8755219612759867 chr13 115169878 11623938 0.10092862996694327 0.9218794255125298 chr14 107349540 8399672 0.07824599900474655 0.8064474266531363 chr15 102531392 8197610 0.07995219649412348 0.7947792692488417 chr16 90354753 14204387 0.1572068599423873 1.4674465996281705 chr17 81195210 8155758 0.10044629479990261 0.9747429100840002 chr18 78077248 5511741 0.07059343331363319 1.34490447768955 chr19 59128983 6471743 0.10945128212335396 1.4935166232870645 chr20 63025520 8982099 0.1425152700049123 1.082163871985466 chr21 48129895 5647351 0.1173356185381248 1.0036133288411815 chr22 51304566 3075646 0.05994877726867429 0.6604373393462193 chrMT 16571 899990 54.31114597791322 46.76987653650285 chrX 155270560 11589347 0.0746396934486486 0.7852655877666951 chrY 59373566 463923 0.007813628711470691 0.3838659050682831