BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173919.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 = 7,388,568 number of mapped reads = 7,148,282 (96.75%) number of supplementary alignments = 772,190 (10.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,586,109 number of mapped paired reads (second in pair) = 3,562,173 number of mapped paired reads (both in pair) = 6,990,998 number of mapped paired reads (singletons) = 157,284 number of mapped bases = 840,760,896 bp number of sequenced bases = 840,238,509 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,614,270 duplication rate = 64.3% >>>>>>> Insert size mean insert size = 974,483.6385 std insert size = 9,193,099.4374 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.5914 >>>>>>> ACTG content number of A's = 251,780,974 bp (29.97%) number of C's = 165,216,125 bp (19.66%) number of T's = 251,684,981 bp (29.95%) number of G's = 171,545,914 bp (20.42%) number of N's = 10,515 bp (0%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 9,152,209 number of insertions = 88,897 mapped reads with insertion percentage = 1.2% number of deletions = 215,172 mapped reads with deletion percentage = 2.94% homopolymer indels = 42.37% >>>>>>> Coverage mean coverageData = 0.2716X std coverageData = 3.8799X There is a 5.5% of reference with a coverageData >= 1X There is a 4.35% of reference with a coverageData >= 2X There is a 3.4% of reference with a coverageData >= 3X There is a 2.81% of reference with a coverageData >= 4X There is a 2.17% of reference with a coverageData >= 5X There is a 1.76% of reference with a coverageData >= 6X There is a 1.33% of reference with a coverageData >= 7X There is a 1.08% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.67% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 62988490 0.25271146666471095 2.8644015241916585 chr2 243199373 79392906 0.3264519353838959 11.777357875935012 chr3 198022430 75437911 0.38095639468720793 1.834601317936067 chr4 191154276 41877959 0.21907937335390812 1.7931998177006034 chr5 180915260 53537001 0.29592308023104297 1.5809885394018715 chr6 171115067 42173385 0.24646213649906118 1.8742014531462214 chr7 159138663 48094188 0.3022156092891141 2.3520157146443914 chr8 146364022 41521225 0.2836846407514 2.7780450612202827 chr9 141213431 36123904 0.2558106813508412 1.9914804284394274 chr10 135534747 37154134 0.27412995429135234 3.610438734362865 chr11 135006516 30991805 0.22955784593389553 1.463766248960835 chr12 133851895 38622404 0.28854581401331675 1.5866157707704809 chr13 115169878 20666688 0.1794452539057131 1.2406031727098876 chr14 107349540 25985159 0.24206120491992794 1.4627951341620316 chr15 102531392 26655401 0.2599730724420478 1.4907070445799342 chr16 90354753 28582807 0.3163398277454203 2.1554778206820933 chr17 81195210 34478311 0.4246347906483646 2.1091286773895406 chr18 78077248 16440653 0.21056906360224173 3.1763732885865843 chr19 59128983 14184212 0.23988594561147789 2.1582404930469927 chr20 63025520 36273339 0.5755341487067461 2.4479812623928514 chr21 48129895 10815540 0.2247156367160161 1.5212055280047057 chr22 51304566 6674743 0.13010036962402138 1.0215357431015974 chrMT 16571 1342759 81.03065596524048 56.156975236141385 chrX 155270560 29085020 0.18731831713622982 1.2675934492510668 chrY 59373566 1660952 0.027974604051910913 1.117351908579994